Yes, there are links floating around to the .02 Beta, the .03 Beta, and the more recent V1.0 Release version of the Stand Alone programmer. I'm pretty sure you can get the .03 Beta to work, but I think it makes much more sense to be running the latest V1.0 release.
If you buy your Pickit 3 from j1sys you usually get the V8.50 MPLAB software on CD. As you (and I) have discovered you should download the MPLAB V8.63 installer from the Microchip website. It seems you need some combination of these two apps to get your Pickit 3's firmware up to date.
-Mike