One issue may very well be the insufficient isolation considering the TX power level. If you really want to run that much power I'd highly recommend having bandpass filter(s) between the PA and the duplexer - this will help reduce broadband noise from the PA. Bandpass filter(s) between the receiver and the duplexer can't hurt either - especially if you're using a pre-amp on the receiver. Oh, another thing - if the receiver natively has a sensitivity of .2uV or better the pre-amp may not help anything but raise the noise floor. If this repeater site is relatively close to (within several miles) of a TV channel 12 or 13 (analog or digital) I'd STRONGLY recommend installing a window filter on the antenna side of the duplexer. The window filter will greatly reduce the "out of band" signal levels for both the transmitter & receiver which will reduce and/or eliminate any IMD issues from those sources. DCI is one manufacturer of window filters for HAM bands (www.dci.ca).
Some folks get all weird about inserting so many filters because they don't "want all that loss." What they don't realize is even with an additional 3dB of IL if it lowers the noise floor for the repeater "system" by 20dB you've made a HUGE improvement in the overall performance. Also, by having 250W transmit power you can easily take a hit and still have a respectable ERP. Good luck and remember.your mileage may vary. 73 Richard