Just to close this one out....
Got in touch with my local Clifford alarm authorized retailer - they told me it would be $400 to $500 to diagnose and repair the problem and I'd probably be better off installing a new system (for an estimated $300).
Contacted another local remote starter installation shop - not Clifford retailers, but they said they'd take a look at it. They quickly determined it must be bypass related and called Clifford support - after 10 minutes on the phone, they reprogrammed the unit and the problem is fixed.
Total cost $25 and I now have my remote start back in time for winter