I had the same issue. Make sure you are running the 7.3 build 555 software. Then you need to upload the most recent firmware to the V2 box. After that, the PCM read will work properly (and do it faster). Look here:
http://forum.efilive.com/showthread.php?t=4158

Also, there are a couple of updated calibration files you need. It works without them, but they enable a few more tuning parameters. Look here for them:
http://forum.efilive.com/showthread.php?t=4310


Since this duramax tuning stuff is still basically in beta testing, it takes a bit more effort to keep each component updated. Once its finalized, I'm sure more thorough directions and a single software update will be included.