Is is strange that I got exactly the same problem thi morning with a MiniProg3 - this time on a PSoC 5 Device.
I found that after my PC had gone to sleep (not standby), when I woke it up I could no longer use the MiniProg3. I had to reboot the PC.
It looks like a bug in the power management section of the MiniProg3 device driver, or a bug in my Windows 7 Home Premium 64b system. I did notice that windows installed 16 Updates last night. Maybe it has something to do with that?