Since the Verify just checks the drive, try using Disk Utility to actually do a Disk Repair, as shown in this link, while booted up on your install disk for OS 10.6.8 and under. If you are running 10.7 or 10.8 run Disk Repair from Disk Utility on your Recovery System. It shows you how in the link.
You could have a little directory corruption that Verify missed and Disk Repair may fix. Let us know what errors Disk Repair reports and if DU was able to repair them. This could just be a start in repairs and you may need a better utility to finish the job.
Then Repair Permissions.
No need to report any Permissions errors........we all get them.
Boot up from your Snow Leopard Install DVD while holding down the "c" key.
Select the language you wish to use, and then choose "Disk Utility" from the menu bar.
Your HD should appear in a panel on the left hand side of the window which opens. Select it and then click on the "repair disk" button in the right hand section of the window.
If Disk First aid is unable to complete the repair you will need to use a stronger 3rd party utility like DiskWarrior or TechTool Pro.
Once this process has been completed restart your computer.
Utilities & info regarding checking your HD space:
OmniDiskSweeper is a free utility that checks HD space.
FreeSpace cost $1 or is a free utility that checks HD space.
SpaceControl is a free utility that checks HD space.