are you really that sure, no just kidding. But I do have the same thing sometimes thinking I had a file, but named it a little bit different or used a space. But I suggest you look in system preferences to see if any category isn't turned on, or that some places aren't searched (second tab)
There is a way to reindex Spotlight but it still will not parse through files in /Library or /System or ~/Library. Also note that Mac OS X Server automatically has Spotlight disabled, not that it seems you're running that OS.
I've reindex Spotlight through OnyX. I have tried to do it the Apple way as well (dragging in and out a folder in the privacy tab). Still, when I am looking for a file in my normal folders (Users>MyName>...), it does not appear.