FWIW, I use a 6" cable with the PK4 all the time. Cables can cause issues, but I don't think that's your problem here.

I still have one bug; 18F4550 programmed by my PK4 run Blinky at 1/2 speed compared to my U2 USB programmer.
Try programming it with the PK4 and then verifying it with the U2, or vice-versa.

Pay particular attention to CONFIG1L. Unless one of them is changing it (????), I don't see how that is.
Are you overriding the CONFIG settings in the hex file with one of them?