@Zidane24,
Well, I just re-scanned setup.exe directly on my x64 system and, again, it got a hit on the Trojan. You're saying you've used this same build without incident? Very odd, indeed! I'm going to fire-up that VM I tested it in originally (prior to launching it directly on its intended upgrade target, my HP Mini 2140) and see if installed MSE into the "infected" VM triggers another hit.
RCK