I've been having this same problem too. I get the error message:
Using cable "ByteBlasterMV [LPT1]", device 1, instance 0x01
Pausing target processor: not responding.
Resetting and trying again: FAILED
Leaving target processor paused
I can program my .sof to the board no problem, I can compile my C application too, but when i go to run the C code on the processor I get that error message. I can't even use the flash programmmer to program the flash memory either, I get an error along the same lines as the one above.
If anybody has any ideas i'd greatly appreciate them.