Well, I had similar issue on my Download folder.
Many times I got the message ' Startup Disk is almost full '.
Finder was showing 37gb on that folder, but, checking each subfolder individually, the size of all was like 10gb smaller.
So, I could not (yet) figure out why it happens, but, I could found 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 '+' button, and add the disk which contains the 'wrong sized folder'. Hit Ok for confirm.
Reboot your mac ( When I learned about it, this step was not mentioned. Did it on my own, just to make sure).
After 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, mountain lion 10.8.5 , 256gb ssd
PS 2 :sorry, I do not remember where I learned it, but, in worse case, you will lost a bit of time while osx rebuild 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'