Wayne, perhaps you can elaborate on exactly what steps you're doing.
I have been able to print and scan/read Atkinson's 4096 patch targets as well as his 1728 patch target (which I use more often, actually), very reliably in strip-mode. I assume you're following steps similar to these:http://people.csail.mit.edu/ericchan/dp/i1...gets/index.html
I also use an Eye-One Pro UV Cut.
The iO sure is nice for automation, but you shouldn't have any problem using the Eye-One Pro hand-held to read in strip-mode. There's something else going on ...
Please elaborate and then maybe we can see what's going on.