You need a generator and UPS designed more toward the commercial market spec requirements.
i.e.
[ul]
[li]More precise generator frequency and voltage regulation[/li]
[li]UPS designed for operation on generator power.[/li]
[/ul]
Lack of generator precision (frequency and voltage regulation) and a consumer quality UPS (lacking adjustable parameters to accomodate generator power) is the issue as pointed out by itsmoked above. The likely end result is the UPS staying in battery mode and failing to switch over to accept generator power.
UPS units for the commercial market will have adjustable parameters that permit operation on properly regulated generators. Namely the window of acceptable frequency, acceptable voltage limits, and transfer delay (amount of time the UPS samples incoming power to determine if acceptable) can be changed per manufacturer recommendations for operating on generator power.
I'm using an older technology, but robust design UPS that came off a commercial job site, a FERRUPs 1.4kVA UPS to power all the electronics in my home. The UPS, with parameter changes per the UPS manufacturer's recommendations for use on generator power, runs fine on my commercial quality generator..