I was unable to reproduce this, but when Factorio crashed, it was half-way through painting a custom GUI panel WHILE the main menu was opened. The only way that custom GUI could be opened in game was by clicking on a custom button (top left). The save file itself has not been overwritten.
crashlog
0.002 2015-08-08 11:51:33; Factorio 0.12.1 (Build 16116, win64)
0.002 Operating system: Windows 7 Service Pack 1
0.002 Read data path: M:/downloads/Games/Factorio/Factorio_0.12.1/data
0.002 Write data path: M:/downloads/Games/Factorio/Factorio_0.12.1
0.002 Binaries path: M:/downloads/Games/Factorio/Factorio_0.12.1/bin
0.003 Info LocaleProvider.cpp:282: Language en is LTR
0.003 Info LocaleProvider.cpp:282: Language en is LTR
0.185 Initialised Direct3D: AMD Radeon HD 7700 Series; driver: aticfx64.dll 8.17.10.1247
0.250 Graphics options: [FullScreen: false] [VSync: true] [UIScale: 100%] [MultiSampling: OFF] [Graphics quality: normal] [Video memory usage: all]
0.450 Loading mod core 0.0.0 (data.lua)
0.488 Loading mod base 0.12.1 (data.lua)
0.609 Loading mod LongElectricBoiler 0.12.3 (data.lua)
0.680 Loading mod LongHelperBots 0.12.1 (data.lua)
0.758 Loading mod LongLargeChests 0.12.7 (data.lua)
0.888 Loading mod LongHelperBots 0.12.1 (data-final-fixes.lua)
1.887 Info LocaleProvider.cpp:282: Language en is LTR
1.888 Info LocaleProvider.cpp:282: Language en is LTR
1.890 Info LocaleProvider.cpp:282: Language en is LTR
1.890 Info LocaleProvider.cpp:282: Language en is LTR
2.369 Initial atlas bitmap size is 16384
2.374 Created atlas bitmap 16384x7660
22.746 Factorio initialised
28.534 Loading map M:/downloads\Games\Factorio\Factorio_0.12.1\saves\Game_x12_HelperBots.zip
28.781 Info Scenario.cpp:160: Map version 0.12.1-4
Factorio crashed. Generating symbolized stacktrace, please wait ...
c:\temp\factorio-ca30f4e3\libraries\stackwalker\stackwalker.cpp (923): StackWalker::ShowCallstack
c:\temp\factorio-ca30f4e3\src\util\logger.cpp (283): Logger::writeStacktrace
c:\temp\factorio-ca30f4e3\src\util\logger.cpp (337): Logger::logStacktrace
c:\temp\factorio-ca30f4e3\src\util\crashhandler.cpp (79): CrashHandler::writeStackTrace
c:\temp\factorio-ca30f4e3\src\util\crashhandler.cpp (137): CrashHandler::SignalHandler
f:\dd\vctools\crt\crtw32\misc\winxfltr.c (372): _XcptFilter
f:\dd\vctools\crt\crtw32\startup\threadex.c (378): _callthreadstartex$filt$0
f:\dd\vctools\crt\crtw32\misc\amd64\chandler.c (162): __C_specific_handler
ERROR: SymGetLineFromAddr64, GetLastError: 487 (Address: 0000000077C7908D)
0000000077C7908D (ntdll): (filename not available): RtlDecodePointer
ERROR: SymGetLineFromAddr64, GetLastError: 487 (Address: 0000000077C68BAF)
0000000077C68BAF (ntdll): (filename not available): RtlUnwindEx
ERROR: SymGetLineFromAddr64, GetLastError: 487 (Address: 0000000077C9DB38)
0000000077C9DB38 (ntdll): (filename not available): KiUserExceptionDispatcher
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1553): agui::Widget::getTopPadding
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (95): agui::Widget::paint
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1281): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1297): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1297): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1297): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1293): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1297): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1297): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1293): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1297): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1297): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1293): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1297): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1297): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\gui.cpp (1025): agui::Gui::render
c:\temp\factorio-ca30f4e3\src\graphics\guirenderer.cpp (35): GuiRenderer::prepare
c:\temp\factorio-ca30f4e3\src\mainloop.cpp (209): MainLoop::prepare
c:\temp\factorio-ca30f4e3\src\mainloop.cpp (450): MainLoop::tickStep
c:\temp\factorio-ca30f4e3\src\mainloop.cpp (533): MainLoop::run
c:\temp\factorio-ca30f4e3\src\main.cpp (398): wmain
f:\dd\vctools\crt\crtw32\startup\crt0.c (255): __tmainCRTStartup
ERROR: SymGetLineFromAddr64, GetLastError: 487 (Address: 0000000077B459CD)
0000000077B459CD (kernel32): (filename not available): BaseThreadInitThunk
ERROR: SymGetLineFromAddr64, GetLastError: 487 (Address: 0000000077C7B891)
0000000077C7B891 (ntdll): (filename not available): RtlUserThreadStart
128.737 Error Util.cpp:45: Unexpected error occurred. You can help us to solve the problem by posting the contents of the log file on the Factorio forums.
0.002 Operating system: Windows 7 Service Pack 1
0.002 Read data path: M:/downloads/Games/Factorio/Factorio_0.12.1/data
0.002 Write data path: M:/downloads/Games/Factorio/Factorio_0.12.1
0.002 Binaries path: M:/downloads/Games/Factorio/Factorio_0.12.1/bin
0.003 Info LocaleProvider.cpp:282: Language en is LTR
0.003 Info LocaleProvider.cpp:282: Language en is LTR
0.185 Initialised Direct3D: AMD Radeon HD 7700 Series; driver: aticfx64.dll 8.17.10.1247
0.250 Graphics options: [FullScreen: false] [VSync: true] [UIScale: 100%] [MultiSampling: OFF] [Graphics quality: normal] [Video memory usage: all]
0.450 Loading mod core 0.0.0 (data.lua)
0.488 Loading mod base 0.12.1 (data.lua)
0.609 Loading mod LongElectricBoiler 0.12.3 (data.lua)
0.680 Loading mod LongHelperBots 0.12.1 (data.lua)
0.758 Loading mod LongLargeChests 0.12.7 (data.lua)
0.888 Loading mod LongHelperBots 0.12.1 (data-final-fixes.lua)
1.887 Info LocaleProvider.cpp:282: Language en is LTR
1.888 Info LocaleProvider.cpp:282: Language en is LTR
1.890 Info LocaleProvider.cpp:282: Language en is LTR
1.890 Info LocaleProvider.cpp:282: Language en is LTR
2.369 Initial atlas bitmap size is 16384
2.374 Created atlas bitmap 16384x7660
22.746 Factorio initialised
28.534 Loading map M:/downloads\Games\Factorio\Factorio_0.12.1\saves\Game_x12_HelperBots.zip
28.781 Info Scenario.cpp:160: Map version 0.12.1-4
Factorio crashed. Generating symbolized stacktrace, please wait ...
c:\temp\factorio-ca30f4e3\libraries\stackwalker\stackwalker.cpp (923): StackWalker::ShowCallstack
c:\temp\factorio-ca30f4e3\src\util\logger.cpp (283): Logger::writeStacktrace
c:\temp\factorio-ca30f4e3\src\util\logger.cpp (337): Logger::logStacktrace
c:\temp\factorio-ca30f4e3\src\util\crashhandler.cpp (79): CrashHandler::writeStackTrace
c:\temp\factorio-ca30f4e3\src\util\crashhandler.cpp (137): CrashHandler::SignalHandler
f:\dd\vctools\crt\crtw32\misc\winxfltr.c (372): _XcptFilter
f:\dd\vctools\crt\crtw32\startup\threadex.c (378): _callthreadstartex$filt$0
f:\dd\vctools\crt\crtw32\misc\amd64\chandler.c (162): __C_specific_handler
ERROR: SymGetLineFromAddr64, GetLastError: 487 (Address: 0000000077C7908D)
0000000077C7908D (ntdll): (filename not available): RtlDecodePointer
ERROR: SymGetLineFromAddr64, GetLastError: 487 (Address: 0000000077C68BAF)
0000000077C68BAF (ntdll): (filename not available): RtlUnwindEx
ERROR: SymGetLineFromAddr64, GetLastError: 487 (Address: 0000000077C9DB38)
0000000077C9DB38 (ntdll): (filename not available): KiUserExceptionDispatcher
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1553): agui::Widget::getTopPadding
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (95): agui::Widget::paint
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1281): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1297): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1297): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1297): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1293): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1297): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1297): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1293): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1297): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1297): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1293): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1297): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\widget.cpp (1297): agui::Widget::_recursivePaintChildren
c:\temp\factorio-ca30f4e3\libraries\agui\src\agui\gui.cpp (1025): agui::Gui::render
c:\temp\factorio-ca30f4e3\src\graphics\guirenderer.cpp (35): GuiRenderer::prepare
c:\temp\factorio-ca30f4e3\src\mainloop.cpp (209): MainLoop::prepare
c:\temp\factorio-ca30f4e3\src\mainloop.cpp (450): MainLoop::tickStep
c:\temp\factorio-ca30f4e3\src\mainloop.cpp (533): MainLoop::run
c:\temp\factorio-ca30f4e3\src\main.cpp (398): wmain
f:\dd\vctools\crt\crtw32\startup\crt0.c (255): __tmainCRTStartup
ERROR: SymGetLineFromAddr64, GetLastError: 487 (Address: 0000000077B459CD)
0000000077B459CD (kernel32): (filename not available): BaseThreadInitThunk
ERROR: SymGetLineFromAddr64, GetLastError: 487 (Address: 0000000077C7B891)
0000000077C7B891 (ntdll): (filename not available): RtlUserThreadStart
128.737 Error Util.cpp:45: Unexpected error occurred. You can help us to solve the problem by posting the contents of the log file on the Factorio forums.