Have a look at Bruce Rozenblit's comments at http://www.transcendentsound.com/power_supply.htm
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In my experience an isolation transformer will not correct or prevent a ground loop hum problem.
My isolation transformers (Xentech Extreme 5 KVA and Equi=Tech 2Q) do make my entire systems sound better by lowering the floor noise which in return gave me more transparency, depth, air, and detail with improved bass, mids and treble.
I'm not sure if this is the type of isolation transformer you're refering to, but I used on of these: Ground Isolation Transformer to eliminate a ground loop caused by my TV cable connection to my HT system. It worked great with no apparent adverse sonic affect.