Hi liastra!
Being that you are at the medical school, I had some questions about doing research for a PI in a different department - how does it work? Does your current PI have a joint appointment with the CMGB department? Did you have to jump through hoops and such to make it happen? Extra signatures, papers, and petitions? Lastly, will your committee be composed of faculty members mostly from the CMBG department, medical school, or MCB department if you were to stay?
I'm extremely curious because I, like you, want to stay in my current department, but I'd like to venture and do research for a different department...
PS if your current department makes you happy and you can do research with a PI in a different department (and his/her research makes you happy and is fulfilling) then do it!