It is very rarely I have met licencing issues with AutoPlant. So not sure what could be wrong. Have you tried to run through licence activation under user account? Go to Licence Management Tool > Tools > Product Activation Wizard.
If it possible, create local standard user for testing. If AutoPlant will work fine with test user, then it could be that the current user has restricted permissions.
Please consider creating service request, as it looks this case will require more detailed analysis.
Regards,
Artiom