Remote Desktop Web Access - Does not seem to access the GAC

Using Windows 2008 R2 and Remote Desktop Web Access.

Using application programs have some 3rd party .NET code loaded in the GAC.  The application runs with no problem by connecting to the server using standard RDP (not web access).

The application runs over Web Access, but does not seem to read the code in GAC because we get 3rd party licensing errors.  Again, we do not get the errors over a standard RDP connection.

Question:  Are .NET 4.0 programs run in a different way when run over Web Access?  If so, how?

Thanks

Tom

MisterT99