I know that Malware.EELY is one of the things that PT3 can be flagged as when it's a false positive. It's in fact the one I've seen the most . . . but I run linux, and Windows only in a virtual machine, so I don't in fact have any a/v software to test it on for you.
But if PT3 is the only infection detected on your machine it's likely to be a false positive (as the only way the PT3 executable could be infected is if something else is already infected . . .)