It's hard to imagine how two different transformers would give such drastically different results unless there was some construction or winding differences between the two.
The only thing I can suggest is:
1) Buy a replacement transformer - you might PM Chunger and see if he has any transformers available for sell
2) Maybe try and improve the shielding on the PSU case. Remove the transformer, and make sure the paint underneath where it makes contact with the case has the paint scraped away.
There's little if any magnetic shielding on the stock transformer but it may help some.
For #2, also make sure that:
a) That the PSU ground node is properly connected to the chassis somewhere (this typically happens right at the 7 pin binder connector
b) that the IEC ground is attached solidly to the PSU chassis.
Maybe you can upload a few photos of these areas?
If you look at Chunger's photo's, you'll see this (on the right side):
Circuit ground goes to pin 7 of the 7 pin connector, which bridges up to the large metal tab (which is the 7-pin housing outser shell), then wire jumpers over to the same shell tab on the 3-pin XLR connector, which then gets tied over to pin 1. All of these nodes need to be tied together.