Hello chimera15 -
Yes, you're correct - when an application developer adds the support for 3D devices into their software, it uses only our basic device driver - only the developer can correct any issues with it.
In general , to check that device settings are are not the problem, you can go back to the defaults for that application by choosing "Restore all Defaults"[3Dconnexion Control Panel – Options- Restore all Defaults] with your application open and having the device focus. A dialog box will then say that restoring defaults will remove all changes you have made to the configuration - confirm to restore defaults.
If you are seeing a problem with more than one application you can use the clean install
steps to restore your device to its original behavior.
If you still see a problem with the navigation, you would need to contact the technical support for Shade12. If changes are needed, it would take a patch or update to the application resolve the problem.