Alt+Tab ↹ functions while in-game, but the window title bar will flicker in the game itself.
Launch SettingsApplication.exe, click on the "Advanced Settings" tab, enable "Manual Compatibility Settings", then tick all the boxes except "Autogen mipmap". Finally, save your changes.
Another popular fix is to simply disable anti-aliasing in the "Advanced Settings" menu and checking the manual compatibility box.
If this doesn't work completely (some flickering still remains), the anti-aliasing can be overridden in the graphics card's control panel.
If anti-aliasing settings don't work for you, try setting a compatibility mode on BGE.exe. "Windows Vista (Service Pack 2)" seems to work well. If you are using a Steam Controller, do not select "Windows XP (Service Pack 3)" or older, as this prevents the Steam Overlay from hooking into the game and mapping the controller correctly.
With this setting, you can also re-enable anti-aliasing.
If you are having problems with the sound not syncing up with the picture, go launch SettingsApplication.exe, go to "Sound Settings" and choose your Sound Card.
Note that using a monitor with a native refresh rate above 60 Hz may also lead to sync issues. To correct this, change your refresh rate to 60 Hz or use an FPS limiting program to set the max FPS to 60.
The unofficial tool "BGAEFix.exe" (by Terry Goodkind) can be found online ("http://www.terrygoodkind.net/~rahly/BGAEFix.exe" or search "BGAEFix.exe Beyond Good Evil"). This tool can patch save games to work around a number of common glitches encountered in the PC game, including: Glitches in the 'Central Hall' area, and the triangle key not falling from the vent after defeating the bots.