Check the VR sense line very carefully. If it is "receiving" a lower voltage than what is actually present, it will tell the alternator to "make more volts" and you'll end up with over voltage.
I had an early failure of my voltage regulator due to a cracked wire (probably from vibration) right where it entered the VR. My high-voltage indicator light came on. This left me halfway to Oshkosh in the middle of Kansas where I finally found a helpful RV builder with an extra VR from a Bonanza that I wired up and flew home.
story here
I ordered 2 replacements (they were <$50) and keep the extra with me in the plane at all times now. FYI - It was a Transpo F7078 model.