Today I had some problems with publishing an internal web site with TS RemoteApp on a Windows 2008 R2 server.
The application is called Maconomy and is partly a Java application.
At first everything looks fine. Internet Explorer launches fine and I could access the web application. But part of the site is using java script which is running as add-on’s in Internet Explorer. These add-on didn’t start when running in a RemoteApp. The application works fine if I have a desktop on the server.
After I had tried a lot, I found the solution. The default icon for internet explorer I was using in the TS desktop was the 32 bit Internet Explorer, and in my RemoteApp I was using the 64 bit IE.
So after I changed the RemoteApps to use the 32 bit Internet Explorer located under “C:Program Files (x86)Internet Explorer” everything works as dream.
Afterwards I found this line : “32-bit processes cannot load 64-bit DLLs for execution, and 64-bit processes cannot load 32-bit DLLs for execution” which is explained here http://blogs.msdn.com/rds/archive/2009/09/02/what-does-64-bit-only-change-about-windows-2008-r2-rds.aspx

Hope this can help others.

/Joachim