you are correct it should be an NPN.
It does seem to control speed however quite well, but i will change it to an NPN non-the-less.
Thanks again...
I hope it is not my power supply, but that would be an easy answer and easy fix.
Well, then that right there is the answer to your mystery. If the circuit was correctly wired, the CCP1 PWM line would do absolutely nothing. For the PNP to "turn on" a current must flow from the emitter, which you have grounded, to the base, which is connected to your micro. That should never happen because whether at 0 or 5v the potential of the pwm should always be higher than the emitter. You need to figure out why ground before the DC-DC is at a different potential than ground after. Looking at the datasheet, I see the converter is isolated. If you didnt wire the before and after grounds together that would explain it, hence the solution is just to take a big wire and attach it to the output ground and the other side to the input ground.
As for why it works with the pickit I have no idea. If I were to take a random guess, I would say the ground of the 48V supply is attached to yoru computer ground for some reason, and plugging in the pickit connects the grounds.