Huh...really...
I've been using my PK3 right alongside of my PK2, back and forth, switching to do this chip or that one. (not in the same instance of MPLAB or whatever IDE I'm using at that particular moment of course).
Have had both PK2 and PK3 plugged in at the same time, each running their own stand alone programmer software direct from Microchip. No problems. eg. burning a PIC32MX with the PK3 and using the UART/Logic tool from the PK2 software on other pins. Works for me.
Google'd the PK3 stand alone programmer software from Microchip, found it straight away, installed it, ran with it.
This was all a couple years ago, been using it since. PIC10/12/16/18, dsPIC, PIC32MX, all no problems with either one, except where the PK2 didn't support whatever chip.
Win 7 Home & Win 7 Pro, both 64 bit versions, MPLAB 1.7x up thru 2.x, desktop PC, laptop PC, direct or thru a hub, doesn't matter...all works fine.
EDIT: DOH! Disregard everything I just spewed forth. Just saw the posts mention Windows 8.1