That is not a problem with RDP but sounds like a general problem with object identification. I'm looking at the sample project that ships with TC 12.5... and I'm not finding any reference to looking for an object as an IEFrame. Have you modified the project in any way from what was shipped? It would be helpful if you could paste screenshots or copies of the code that is being attempted at this point.
I, just now, tried running the script on an RDP instance to a Windows 7 box that I have. I don't, currently, have a Windows 2008 machine available so I can't simulate EXACTLY... but generally speaking, your issue is not with RDP nor with the project shipped with the application, but something going on with implementation within the project.