Would it be possible that it's actually not the folder you noted (i.e. the last folder you saw in the progress box), but rather the next one? The progress display is not updated immediatelly (in 1 second interval maybe). I'd suggest to check a few folders that may follow the "last" one.
What operating system do you use? If it's Windows NT/2000/XP, the files/folders should be enumerated alphabetically.
Also, make sure you use the same sensitivity (quick/standard/thorough scan, setting of "archives") when checking for the "bad" folder, as you used in the full scan.
Thanks.