I was not able to get my PICkit3 working with a Windows 7 64 machine. Though I tried different suggestions offered at the Microchip forums, the error seemed to be the one shown below:
I found a possible solution to this issue. I downloaded the PICkit3 GUI and scripting application from here.
I extracted the PICkit3 application and launched it. Under tools, there was an option called “Download PICkit3 operating system”
There was a file called “PK3OSV020000.hex” in the PICkit3 GUI directory. This hex file updated the firmware on the PICkit3 and this solved my problem!