I had a couple of problems with my Warp13 programmer (serial port based) that caused me some headaches until I figured out that it was junk running in the background, mainly those programs that monitor cpu temps, fan speeds, etc. were causing it to mess up. Try killing all your background processes (well, not all, but at least everything in the tray) and then trying to program. heck, boot up in safe mode and see what happens.
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