I've seen other posts here and in the GPS forum that all basically state the same problem... Mobile PC just likes to sit on top.
I'm having some success with covering parts of it with a simple OSK that looks like a menu skin. OSKs seem to be the only thing that will sit on top of Mobile PC and still allow the user to interact with it. It's a cheesy solution, but it'll keep me going until a clever skinner or programmer starts digging into it. I guess we wait until Mobile PC becomes more popular.