George,
I'm not sure if I can be of any help since I've never faced such a problem. However, have you tried calibrating your pickit3? I do not have a pk3 but, in the pk2 there is a calibrate function where you can set up the voltages accurately. It is under Tools->Calibrate VDD and set unit id on the pickit2 software.
Maybe the VIHH needed for programming the part is off?
Best
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