OK, that model handles up to three cooling & heating zones (a/c units). The EC-30 shuts off the genset when the a/c is no longer needed (thermostat is satisfied). If another a/c zone then says 'not satisfied', it would start up again. But if the other zone a/c is already running and still not satisfied, the EC-30 is supposed to use what it calls "adaptive management" to avoid "short cycling" (what you are observing) and keep on running.
So, if you have 2 or 3 a/c running and the EC-30 shuts down as soon as the first one stops, either it is not wired to the zones properly or it is defective.I don't know enough about it to tell you how to diagnose which it is, so I suggest consulting with both Onan and Winnebago about how it determines the a/c status.