I'm still betting on the Time Machine backups being the issue. Apple sometimes "adjusts" reported free space to try and remove this space, though I've seen it get (temporarily) fouled up about this number. So, for instance, Finder does not count such space as used, but Disk Utility will show it as used.
Those backups are written to "/.MobileBackups" which (kind of) shows up as the "MobileBackups" drive you will see from time to time. Although items are written out to it and some deletion compression takes place, like your external Time Machine the general rule is that this thing will continue to grow until it (eventually) fills all available space. That is by design.
The MobileBackups disk you see in OmniDiskSweeper is the mounted version, and it doesn't appear you will get useful information if you "size" that volume. However I believe you can get the "real" size of the MobileBackups from a couple of places.
Officially, About This Mac->More Information and then Storage will tell you about the backups on your flash drive. That's *usually* correct, though I've seen it get lost on the machine I'm writing this on. I suspect that's because the machine had been set up using Migration Assistance from a MacBook Pro that had been running Lion for a while and some of that information may have "tainted" the starting point. Now the system appears to have finally figured out the real space used :-) .
I'm not sure it's more reliable (since now everything appears to work fine), but you might also get some information if .MobileBackups is involved by running the command in Terminal to show the size of that directly (Finder won't show because only root has permission to look at it).
I first fired up Terminal to get a command prompt. From that prompt I entered the following:
sudo du -sk /.MobileBackups
You will be asked for your password to authorize the command, but by the Terminal (not the standard OSX dialog).
When it ran (took a short time) it output the following:
Which basically agrees with the 2.8GB of backups that About This Mac's More Information screen comes up with now. And which Finder totally ignores and treats as not used.
If your drive has as much free space as you expect it should have and either you've had the machine for a while, or you've downloaded and deleted a buch of videos in a directory that's not excluded from Time Machine's backup routines, I could see those "there but not really" files (at least as OSX seems to view them) easily growing to be a pretty good size. As I noted, if this is the problem OSX will kick parts of that backup off the drive as more space is needed--it's holding them there "just in case" you might want to restore them.
Have you actually had OSX complain about not having enough free space on the boot drive?
What I have found with Lion is that trying to reconcile various utilities views of free drive space can quickly drive you crazy :-) . The cause always seem to involve accounting for that mobile version of Time Machine backups.