Most people I've talked to said that's generally the problem with old synths (it fixed my prophet 600), but alas, the MKS is still jacked.
No slam, but I repair synths for a living and don't recall having to replace a power transformer in any synth in well over 5 years.
It's not a "general" thing. It's quite a rarity really.
Misdiagnosed synths problems are pretty common though.
I would suggest actually testing the transformer before considering its replacement.
It's quite easy to test using a dual trace scope.
Your symptoms could also be a bad rectifier, transistor or power regulator.
Also since you say all the caps were replaced previously, I'm hoping the tech knew that one cap goes in backwards normally on one rev of SupJup - the silkscreen is wrong.
Best of luck,