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In my experience using VMWARE, after the board is programmed, depending upon the hiccup that OSX gets on the USB disconnect/reconnect (due in part to the software the board is running), the virtual handler may not automatically reconnect the "new" USB device to your windows virtual machine.
See if parallels sees the USB device as some new device. If so, see if you can tell Parallels to reconnect the device to the Windows machine automatically when it sees it. Do that for all the USB devices that the board presents to you during your testing.
That *may* allow the programmer to talk to the device and cause it to be programmable again. I'm not certain this will work for you, as I am not familiar with Parallels, but this kind of problem presents itself with VMWare also.