Short answer: Get a new IS guy j/k

You might want to show them my message, or point them to the Citrix web site for a more complete explanation. Unless they are short on available drive letters to map (don't laugh, I've been at clients who mapped a seperate drive letter for each application they had installed, ie W: for WordPerfect, L: for Lotus, etc), they should be able to set up the rootdrive function and give you that functionality without affecting any other applications already running.
In case they are getting into that "you're a programmer, what do you know" mode - my main job function is installing Citrix and NT networks, I do a LOT more of that than I do programming. I've found it very useful to be able to look at things from both sides.

Randy