Why is your FOB only working intermittently? Battery on its way out? I'd start there first.. I hate when those things don't work.
In regards to the window.. is your rear wiper correctly resting on it's peg? If I recall correctly, doesn't that thing have a sensor in it that wont allow the rear window to move if the wiper is in use (IE; not "docked")?
I could be wrong.. but I thought I had read about that at some point.