Nearly a year later in this topic and I have just installed 5.3 on a new pc, having previously run it without any problems using XP SP3. I now have a new PC with Windows 7 Pro 64 bit and once I installed Sitemapper 5.3 it started displaying all the problems described by Steve Houseworth, I even had my pc completely crash, only to be revived by safemode, system restore and so on. The installation also seemed to cause a fragility and unstable behaviour in my machine which put me in mind of some earlier Windows releases.
However, I re-installed and ran the compatibility wizard, installing as XP SP3; result is scans that work every time and no crashes. Seems that it's always worth checking the compatibility wizard.

One of the things that marks a difference of Windows 7 is that a good handful of programs (CC programs and other programs too) sometimes require just the "Run as Administrator" box checked and then work just fine. Might want to see if that is the issue for you too instead of running it as XP compatibility, although that will probably work just fine too