A game may receive both the physical and virtual controller, or multiple mappers may be active. Test with one mapper, review Steam Input for that game and configure HidHide so the game sees the intended output while Nexus retains physical access.
Check which profile is applied after the game gains focus. Auto Profiles may switch it. Duplicate a profile before experimenting; do not delete AppData as a first troubleshooting step.
Still stuck?
Prepare a support report or return to the troubleshooting hub. A browser controller test can help observe input, but does not verify Nexus mappings, virtual output or every feedback feature.