Jbfan,
The tech is probably right. If the UPS does not have an input filter that is interlocked with the ATS then it is very possible your problem is an undersized generator. What happens is the UPS throws lots of harmonic current back on the system and this causes havoc with the generators regulator. The fix in the past has been to double the size of the generator to compensate. The newer large UPS’ have an input filter that allows you to size the generator closer to the load. I don’t have any back up literature handy but if I find it I’ll post back.
Nick