You are probably the ONLY person who has actually had this happen.
I have to agree with Randy on this. In the 13+ years I've been using DCC and following DCC-related forums, etc, I've only heard of one other possible ground-loop issue, with an MS100.
Unfortunately, the person reporting it never offered details of their wiring configuration, so it was impossible to know for sure that it was caused by a potential ground loop situation, or by something else.
But in my 13+ years of using first an MS100 (I bought it at the same time I bought my SuperChief) and then a PR3, I've never run into this myself. And my layout computer is even on a different branch circuit than my DCC system. For all I know, it might even be on a different phase. I've never needed to check, because it's never caused any issues.
The important thing to remember is that the unfortunately-labeled "Ground" on Digitrax equipment is actually an "equipment common", which as the correct name implies, is meant to give all connected equipment a common base reference point. That "equipment common" does not need to be "grounded" to the house current ground, and in fact it should NOT be unless done correctly. This comes up often enough on the Digitrax Yahoo list that a "Grounding and Commons" best practice document has been placed in the Files section.
Having said all that (Whew!), if your layout and DCC equipment are wired properly, the ground-loop risk is minimal to none, and as Randy also mentioned, the benefits of the PR3 far outweigh any such risk.