I appreciate very much all of the feedback and suggestions. After working with it for another day, I believe there probably are some software issues, but I believe the device itself may have some problems based on a couple of things.
Last night, I had a couple of occasions were it failed to read the first strip if the 3rd page. Rather than trying to take 5 readings, it moved back to the calibration pad, then tried to read it again, this time moving at an incredibly slow speed (I would say 1/15th or worse of normal speed). It sounded strange, and then would error out with the too many errors message.
I shut everything down, and brought it back up. At this point I can no longer read in a test I did a few days ago without any problem, it errors out on the second page. It seems quite possible that something in the device is wearing or is loose, and causing tracking errors that are getting worse.
However, to confuse the issue, I switched to the revision A, which Andrew suggested, and while it reads much slower, it was able to read in the Canon paper that I was never able to read in with the Rev. b. So for now at least it is usable again. I don't have a problem using the rev. A, but I'm worried that whatever reason has suddenly made it unusable with the rev B device may eventually show up and make it unusable altogether.
I guess despite my claim yesterday, after seeing some comments here it seems that x-rite may be abandoning the device, I am beginning to regret not going with the iSis. My dealer is contacting their distributer. He wasn't too pleased at my issues, and is going to push the distributer for either a new one, or a full credit towards an iSis. From what I"m reading here a new one may not be possible, so at this point I'm hoping the iSis option opens up. I'm sure I won't be that lucky but I'll keep fingers crossed.
Thanks for all the help.