Another thought about qualifying to attest for the July-Aug-Sep quarter:
In the
link to the CMS document provided by Mark@ AC above, look at this statement near the bottom of page 27: "At the EP?s discretion, the numerators and denominators of certain measures may be calculated using only the patient records maintained in certified EHR technology. The EP may also elect to calculate the numerators and denominators of these measures using ALL patient records." My interpretation is that running a report using the AC Reports Module (NOT the MU Wizard) to find the number of patients that meet a certain criteria in that time interval is the numerator, and ALL patients seen in that time is the denominator. You can report those numbers even if the MU Wizard didn't save them correctly.
I realize that this is not what you were told by your Regional Extension Center, but I don't think they understood your problem. You do have a non-zero numerator for these measures; its just that the MU Wizard didn't save them correctly.
Just a thought. Good luck.