Errors upon erasing free space

I have been experiencing particularly bizarre errors since switching to Mac. Two of the strangest are related to erasing free space.
I wasn't aware that OS X could erase free space on its own, until I read the security guide, so I first purchased Shredit X. It worked the first time. The second time, it did not free up the space after the shred. I couldn't even close my programs without resorting to the command line, but I eventually got it to shut down without a hard reset. As I was logging off, the "Reclaiming disk space" process, or whatever it's called, ran as usual, and it appeared to work. My disk space was back to normal. A few days later, I tested it again, to see if it was a fluke, and it did the same thing. I have spoken with the company, and they're not sure what caused it. So I decided to go with Disk Utilities instead.
I started the process last night, and left it going overnight. This morning, I checked to see if it was finished. The login screen that appears after the computer has slept worked fine. However, it was a different story after I logged in. I could not hit any key on the keyboard, and they would trigger the beep that occurs when you hit an invalid key. I could not left-click. The only input that worked at all was a right-click, and it only worked on the application bar at the top of the screen. I was unable to shut down, because I could not close dialog boxes, so I had to hard reset.
It would be nice if there was some explanation for either of these...

<EDIT>I don't know if I made this clear enough in my original post: The computer works fine after the restart, and I am even posting from the computer in question right now. The problems with input lasted only between the time the free space wipe finished, and the time when I had to hard reset.</EDIT>
The Knowledge Base article about Disk Utility to which you linked stated this: "When possible, disk permissions should be repaired while started up from a Mac OS X volume (hard disk) that contains updated Mac OS X software, instead of a Mac OS X installation disc." It also mentioned loss of software updates if it was not run from the startup disk. And so, I am a bit leery of running it from the install disk...
I had verified disk permissions a short while ago, so I didn't expect anything out of the ordinary. I was wrong, and there was quite a bit of weirdness with the permissions, almost all of it about not expecting ACL in "System/Library/User Template". I tried to repair disk permissions, and everything looked like it went okay. But when I verified again, it apparently didn't actually repair them.
Will running Disk Utilities from the install disk cause me to lose any data? I have no backups, as I don't own an external hard drive, so I really wouldn't want to lose anything. In particular, my collection of images of album covers, my music collection, my own recordings, and the metadata on the music are all things I'd rather not part with. Should I even be worrying about this?
I'm also not sure what the connection would be between my problem and disk permissions. Could you explain that a bit? I still have no idea why erasing the free space messed with my input devices.
Sorry for the extra-long post, but I figure getting as much info out as possible could help to solve the problem.
That animated image of a bug in your signature is amusing, by the way.
Message was edited by: Your New Favorite

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