Given that on-the-fly partial reconfiguration is a feature that requires a license you would have to buy from Xilinx, you should discuss this problem with your Xilinx FAE. When I used this functionality a few years ago, the license also included a 2-day training course and lots of tech support from the FAE's.
Talking to them would definitely be your best bet, since you have really not given us enough information to even make an educated guess at what is wrong.
r.b.