I'm having this same issue. I have a Canon all-in-one. Even though the neat scanner is showing up in the System Profiler (as "600dpi USB Scanner"), the only scanner the NeatWorks software can find is the Canon. When I unplug the Canon, it can't find any. Un+re-plugging the neat scanner doesn't help.
It's not feasible to reboot and unplug each device to get NeatWorks to find the desired scanner (especially with Mac OS X where you rarely need to reboot, even while installing new applications, etc). Please fix the bug!
