Hm... could it be that this bug appears after you unplug a controller and disappears once you go to the settings page and save (don't even need to change anything)?
@ruger392: Instead of deleting everything in the AppData folder, deleting (or renaming) the fs2_open.ini is probably enough. Would be interesting to see the difference between one version that causes the bug and another that works fine.
I've done some more in-depth testing and come up with some interesting results.
If I delete fs2_open.ini, connect a new controller and disconnect the previously selected one, then start Knossos, then run a mod, the game launches fine. If I try to start it again, I get the bug. The newly created fs2_open.ini shows
If I then select the new controller in settings and save, fs2_open.ini shows
If I then start a mod, it launches and fs2_open.ini changes to
From there, the game launches every time and has no problems.
If I disconnect the selected controller, the game still runs. If I save settings without changing anything (the joystick drop-down is blank), I get the bug and fs2_open.ini shows
If instead of saving settings, I restart Knossos, I get the bug and fs2_open.ini shows
Reconnecting the controller doesn't change anything. Saving settings without changing anything (the joystick drop-down shows the controller) doesn't help and fs2_open.ini shows
Switching the joystick to "No joystick" and saving allows the game to launch. fs2_open.ini shows
Re-selecting the controller and saving yields the bug and
Manually setting CurrentJoystickGUID to 030000004F040000FFFF000000000000 doesn't help.
With CurrentJoystickGUID=4f04ffff000000000000504944564944 or CurrentJoystickGUID=030000004F040000FFFF000000000000, restarting Knossos from that point allows the game to launch and everything works fine.
Working and bugged fs2_open.ini files attached (in an archive because the site wouldn't let me upload .inis)