That sounds like quite a peculiar issue you're facing. Since you have ruled out quite a substantial amount of possible reasons and your stereo channels only swap when running 3D applications, it suggests perhaps the scenario has to do with how 3D sound is handled or processed by Windows and your audio drivers in those applications.
Here are some suggestions to narrow down potential fixes:
1. Compatibility Mode: Perhaps the 3D audio processing in some games is an issue for your Windows version, and running the game in compatibility mode may help.
2. DirectX Check: Some 3D applications sometimes utilize older versions of DirectX for 3D audio handling. It would be wise to ascertain the DirectX version every game is using and see if there...