A few questions to clarify the situation:
1. Is this the first time use of the UPS"s and this generator?
2. What size and type generator.(home use or commercial duty)?
3. Professionally installed transfer switch?
4. Did you try to check waveform with O'scope?
5. Are all the UPS's on the same phase (even or odd numbered breakers)?
6. Are line conditioners the constant voltage transformer type or a inverter
It does sound like that if you have a quality gen set that there is a problem
with the neutral. You should check all neutral connections and also confirm
that the neutral is not bonded to ground at only one point. Sometimes gen sets
come with the neutral grounded for stand alone setups and this bond point must
be lifted for use with transfer switch where the neutral is already bonded at
utility service. Since all the regulators in the system use the neutral for
zero volts reference, the generator regulator may be fighting the UPS's
regulators on a 60 cycle basis and creating phase noise. It all depends on
whether zero point crossing regulators are used.
This is all a guess, without actually being there when it all happens.
Hopefully all that died was UPS's and not expensive Steppir controller or
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