Well, I had similar issue in my Download folder.
Many times I got the message 'Startup Disk is almost full'.
Finder was showing 37 GB in that folder, but, checking each subfolder individually, the size of all was like 10 GB smaller.
So, I could not (yet) figure out why it happens, but, I could find out how to fix it.
The only matter is the problem may keep showing itself up.
So, to fix this, go to 'System Preferences' -> 'Spotlight', then, 'Privacy'.
Click on the '+' button, and add the disk which contains the 'wrong sized folder'. Hit OK for confirmation.
Reboot your Mac (when I learned about it, this step was not mentioned. I did it on my own, just to make sure).
After the reboot, go back to system 'System Preferences' -> 'Spotlight', then, 'Privacy'. Now, click in a disk you just added, and remove it (using the '-' button).
And it's done the trick.
PS 1: MacBook Air 2010, OS X v10.8.5 (Mountain Lion), 256 GB SSD
PS 2: Sorry, I do not remember where I learned it, but, in the worst case, you will lose a bit of time while OS X rebuilds the file indexes to improve spotlight search.
PS 3: If you realize the spotlight is not searching how should be, it is a signal that above procedure should be executed.
PS 4: Another tip that may be helpful:
Go to Disk Utility, select your disk, and hit 'verify disk permissions'. After done, click in 'repair disk permissions'.