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 is a pattern.
3. Game-Specific Settings: In case it's an in-game audio setting causing the swap in certain titles, exploring the game's audio settings may prove worthwhile.
4. Third-Party Software: Consider using a third-party audio manager, possibly one that can specifically manage 3D audio settings.
5. Windows Sonic/Dolby Atmos: If you're running Windows 10 or later, these are in-built solutions that handle spatial sound and you can try activating or deactivating them.
6. GPU settings: In some systems, the GPU drivers can have specific settings for 3D applications. Depending on the GPU you're using, you might want to check if such settings exist and how they're configured.
If none of these suggestions alleviate your issue, it might be a unique compatibility error between your specific software/hardware and Windows' 3D sound handling. You may need to conduct more in-depth trouble-shooting or seek direct assistance from Microsoft's support team or relevant game developers.