I would say the icons should be part of the actual machine, why would this not be the case?

This has been verified in chemical plants and assembly machines, probably happening on all machines.

The player is rendered behind the side walls of the gate.

I am using Linux (if that matters)

When using the arrow keys to browse through the list of mods, or clicking on different mods, after a while, the game crashes and produces the following error message in the log:

http://pastebin.com/VymCA4Nk

Installing mods works fine.

Edit: Note: The log shows mods, but the issue is also ...

Yes. that worked! Thank you!

The crash is for all scenario packs, my factorio version is 0.12.8, the most recent unstable. Would be a shame if I need to downgrade to a stable.

I Reinstalled the game, it still crashes.

When I load it, it comes up with a dialog box telling me an unexpected error occured.

Here's my log file:

0.001 2015-09-24 16:20:59; Factorio 0.12.8 (Build 16825, win64)
0.001 Operating system: Windows 10
0.001 Program arguments: "E:\Program Files\Factorio\bin\x64\Factorio.exe"
0.001 Read ...