You can download puck diagnostic software from Xrite.
You mentioned the charts are the right size. I assume your horizontal patch size is no more than 9 or 10mm. I had some trouble with oversized patches, the scanning software is very sensitive to that.
edit...and on my Win7 system the puck driver will time out after a period of time and stop working properly, although it still seems to be alive at some level. Very strange behavior, but unfortunately real at least on my system. The fix is to unplug the puck and restart i1Profiler.