Are you a Generac dealer ? I ask this because the last time I had a problem with a Generac generator the first question I was asked by the factory was "Are you a dealer"? Supposedly, if the generators are not started up by a dealer there could be warranty issues. Anyway, I had a 13 KW generator engine throw a rod after being installed for 4 months. It never ran under load. I had purchased the generator "on line" and installed it myself (except for the gas line) and thought it was a pretty good install. When the dealer's rep. got there he pointed out 3 or 4 reasons why the unit threw a rod and one of which was an incorrectly sized gas line. Long story, short they stood behind their product, I corrected the gas line size but it took 3 months to get the generator repaired.
Anyway, from my experience the voltages shouldn't be more than a volt or two apart. Re-check the voltages again at the generator in both exercise mode and under load. Also, check the connections at the 1st connection port (they're usually not the greatest). If you're still getting a flicker, disconnect the wires from the load side of the generator breaker and temporarily connect a keyless fixture with a 60 watt bulb right to the breaker and run it in exercise mode. If you are getting the flicker there then the problem is in the generator. If not, reconnect the wires in the whip and connect the keyless fixture right to the xfer switch (be sure to shut off all the breakers). If you still have the flicker then the problem is in the whip. If not then turn one breaker on in the auto xfer switch and connect the keyless fixture there to see if you have the flicker. If you get the flicker there the problem is in the xfer switch.
If you are able to narrow the problem down to a Generac part you'll have to contact a dealer to make or provide any corrections or replacements.