I seem to be having problems using the new PICKIT3 Scripting tool v3.00 BETA and the PIC32MX1/2 series (or at least the PIC32MX250F128D) . This is my first attempt with the PIC32 series and so I wired it will all the necessary connections (including decoupling caps between VDD and VSS and 10uF tantalum on VCAP/VDDCORE) on a general purpose (aka prototyping) board. Everytime I attempted detection of the PIC32MX on my development board it would fail asking me to check the capacitor on VCAP. I verified and re-verified the connections and the darn thing would still not detect it. After wasting more than a couple of hours and considering the possibility of having a spoiled uC, I just fired up MPLAB and voila it detected the device. I was able to get a basic LED test routine working without issues.
So it looks like the PICKIT3 Scripting tool has issues with the PIC32MX1/2.
I am posting this just to ensure that others do not run into the same problem.