Just to add another data point, upgrading to the full RGB module (my "Design" package only allowed the 45 patch RGB and CMYK targets) finally gave me the option to load in the larger external data file created by MeasureTool from ProfileMaker. When I ordered the upgrade online (X-rite didn't want to do it over the phone), I asked in the comments box on the ordering page if I could use my coupon. It took a few days extra and I had to email an image of my filled-out coupon but I got the upgrade for $99.50 plus tax versus $199 plus tax. Bottom line, if you still have the coupon, try using it.
I too am also experiencing the problem where my i1 Pro does not like Bill Atkinson's 1728 targets and gives me the "too many errors" (I think that is the wording) message when I try to scan a full row at a time. I wrote Bill and asked if he had heard of other i1 Pro users who were experiencing this problem. He wrote back that he wonders if something has been changed in the coding for the more recent versions of MeasureTool. The additional thought that others have brought was whether the problem only happened with certain revisions of the i1 Pro. Bill wrote it would probably take a rewrite of the targets which, understandably, is not a priority for him since he now measures using another device.
I will have to try holthaus' suggestion to print the targets a bit larger and see if that helps. Thanks to holthaus and everyone else who has contributed to this thread!
Doug