An interesting article has been released today on technet about the mutiple credential prompt when using RD Remote apps. It describes the a solution that is documented in KB977507 and envoles editing the renderscripts.js which is located in C:\windows\Web\RDWeb\Pages\ on the RD Web Accces server.
If you have mutiple credential prompt issue it will be worth a try!
You can find the technet article here:
And you can find the KB article that it refers to here: