>>The "flat on the glass" scan was dramatically clearer than the others. No comparison.<<
99 out of a 100 times when there is a huge difference as you describe it is due to the fact the software settings were wrong. If you had the film in a film holder and got the bad results then you most likely did not set the software to "film with film holder" and instead had it set to "film with film area" guide.
Even the Aztek demonstration page made this same error (unless they have corrected it since I last visited).
Doug