This might well be due to other settings/variables being set when you start NX.
You should compare you NX syslog from you Native Session to the one starting NX Managed (TCIN).
Or post the 2 syslogs here, so we can have a look.
But look for 3Dconnexion and the settings in the syslog.
Make sure this variable is being set correctly:
It should point to the proper 3DxNX.dll
Another issue we've encountered (probably not your issue, but one never knows)...
The way we keep track of updates to (Moog customizations to) Teamcenter requires TC be run as Administrator. But the Spaceball service is started as a "regular user". So it is not available to NX (when started from TC). I believe the fix is to have the TC startup script stop & restart the Spaceball service. As it is restarted in "Administrator" mode, it is then visible to NX
Production: NX10.0.3.5 MP16/TC11.2
I'd rather be e-steamed than e-diseaseled