I had a similar long-term issue with my Inter-Av acting up. I replaced the regulator, overhauled the alternator, and replaced circuit breakers. The only thing left was the over-voltage relay, which Inter-av told me never goes bad. I even tested the over-voltage relay with a variable power supply, and it cut out at 16VDC as it should.
Finally I replaced the over-voltage relay and the problem was solved. I believe the contacts of the relay were chattering during flight due to vibration since it was mounted on the interior firewall. Perhaps as a test you could remove the OV relay from the firewall to isolate it from vibrations and see if that cleans up your electric.
I got rid of the Inter-Av several years ago and went with Plane Power after the Motorola alternator began to eat brushes, I have been happy ever since.