Probably part of the security problems of Windows is that there are many different ways to hide things from the standard tools that manage the computer. There are hidden services, hidden programs, hidden files, hidden flags and attributes and any number of stealthy paths open to be exploited by malware. Microsoft set them up with the best of intentions, I'm sure, but in the end, they are far more useful to viruses than to the owner of the machine.
Mokalus of Borg
PS - In fact, I'm pretty sure they were set up to hide things from you.
PPS - Well, maybe not you, specifically.