Long story short, I had pretty much the same issue with a York Chiller and a Trane chiller, the York was an older centrifigual with the wrong CT on it(half the size it should have been). When it would start it would cause the controller to read wierd, cut inputs on and off and all kinds of stuff. My contoller took 0-5VDC as an input, on startup the CT would generate 14VDC
What year is the generator. Back in the day we had issues with shielding generators causing interference with electronics. Sometimes you could provide a better ground for the gen set and it would get rid of the issue. Then other times you had to isolate the ground to prevent interference.