That could explain the save and achievement data, but what about the launch configuration issues? I've uninstalled and reinstalled. Same windowed mode and loss of customized settings every launch.
This is probably a permissions issue where Factorio can't write to the config files. Backup your save ...

That could explain the save and achievement data, but what about the launch configuration issues? I've uninstalled and reinstalled. Same windowed mode and loss of customized settings every launch.

Game was launching, saving, and running fine up until yesterday.

Steps:
-I saved my game as per usual and shut down PC for the night.
-Upon launching the game the next morning, the game opened in windowed mode, and loaded all the mods I had previously used but had disabled for my current play ...