IIRC the PicKit3 stand alone GUI program and the command line app PK3CMD.EXE are limited to older devices. If you want to program the latest devices you need to soil your self with IPE or look at PicKitPlus (which breaths new life into Pk2 and Pk3 and well worth the price).

Note that for some reason known only to Microchip, IPE writes different firmware thus screwing the GUI version.

Ditto mpgmike's comments. Definitely try different USB ports and Pic devices, even better try a different PC.

What Pic device are you trying to program?

BTW many current Pic devices will program with very low voltages. For instance I regularly program 18F25K50 locally powered with 3.3v.

Edit. I forgot you can tell the Pk3 not to provide Vcc.