Late as usual, that's me. Seems most troubleshooting has already been covered. There are a couple of points that need to be stressed though. First and foremost is to check the incoming line for balance. If it's not within 5% or so, scream at the utility. Load balance matters too, but is harder to check. The utility can do it if you don't have an electrician "in house". An "amp-probe" will solve many such problems. But getting into the "entrance" is dangerous. Best electrician is an old timer that shows up with a Simpson 260 and a magnetic Amp-probe. Don't trust the man with a digital anything.
Then you mentioned 460 wye connected with step down or isolation taking place. And a couple other anomolies. Up front was recent work. Is there any way to isolate the "new work" and try the older system? Then there is the compressor(?) slapping the wires when starting. That is a no-no by any measurement. The starting load can be as high as 500% for starting. It doesn't last long, but is a major consideration when sizing wire.
Then the last thing bothering me is the possibility of "delta" distribution from a "wye" source. How old is the original electrical plant? If it is 40-50 years, or more, old, there may be a "grounded delta" system in the mix. Grounded delta was outlawed years ago, but existing systems are "grandfathered" and still allowed. It is seldom (if at all) taught and few are even aware of it. It has a valid reasoning for being used but is highly dangerous. One leg(phase) is intentionally grounded. In a mixed system with wye and delta distribution, strange "electrical phenomena" can occur.
Just remember, you titled the message "Electrical Mystery". That is not so far off the mark, electricity does weird things. When you have solved the problem, the answer is obvious. But finding the answer may well involve standing on one leg, with the opposite eye closed and chanting an Egyptian mantra while holding your mouth "just so".
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