Ditch JungleFlasher and Windows. Make a DOS boot disk. I had a lot of trouble, until I gave up trying in Windows.
Also, put pin 3 back in. Boot the comp into DOS with the 360 already powered on. When you get into DOS, just eject the drive with the 360 and push it halfway in, pull the drive's power cable, wait a second and reconnect it. Connect your serial cable and probe. Run dosflash. That's all it took for me, got a good key first shot with that procedure first time trying in DOS... after almost 5hrs messing around in Windows.
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I had the same problems in DOS as well (about 1/2 attempts were in Windows the other half in DOS).