Well, I'm sure not gonna tell you I know or have seen everything, but I've never heard of a transformer that did NOT want its frame bolted to the chassis with authority, both mechanically and electrically.
I'm sure you've read plenty of things that reco as a "best practice" in builds orienting the fields of chokes, OTs, and PTs in ways where one cannot (or should not) induce a field into another. Does this line of thought make sense?
Any chance of having enough lead length on your tranny to try rotating it 90 degrees as a test? (clockwise or c-clockwise as viewed from the top...not as viewed from the side)
Was the tranny originally a "through-chassis" type, eg; like a stock Super Reverb PT and now you've changed to an "upright" style like a stock Super/Twin Reverb >>OT<<? In other words, is there a big rectangular cutout in the chassis or are there only two relatively small holes?
Still seems pretty weird and I imagine, frustrating.
Would it be too bizarre to contemplate placing a bent piece of sheet metal between the PT and the rest of the amp to see if the shielding factor changed anything? Yeah, I know it seems weird but if you have something like that laying around (could be a bent-up pie plate for pity's sake) you could just throw it in there while the amp was working and see if it made a difference. Has to be grounded, of course.