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Ok, there is actually 1 file reported by DIR, and the two directories contain 5 subdirectories. 21 directories if you count . and .. as DIR does. ATTRIB /s /d reports 12 entries, including the recycle bin and system volume information.

Still, 12 is not 11237. And defrag (windows 7) reported that this external usb disk was 75% fragmented. Defrag took around an hour, but after defrag the disk is 0% fragmented, and fragmentation analysis now takes seconds instead of minutes.

The recycle bin is empty (and I've deleted it to get rid of the user entries).

Question: what was fragmented? Why does chkdsk report 11237 files?

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Can we see the exact chkdsk output? – TheBlastOne Oct 16 '12 at 5:47
If chkdsk says "11237 file records processed", that does not mean there are 11237 files. – kreemoweet Oct 16 '12 at 6:46
System Volume Information can have all sorts of crap in it (like snapshots, system restore info, etc.) that is not listed via ATTRIB /s. Just delete this directory (and it may require some magic to do so). If you want your external USB disk to be completely empty, just reformat it. :) – MJZ Nov 30 '12 at 22:43

This USB disk had been formatted as NTFS and attached to a Synology NAS (Disk Station). Where it was used as a backup destination.

Disk Station was configured to backup up file permissions. (At least some of the files had ACL file permissions). It created 11 thousand unmovable hidden permission things, which are shown by an alternative defragmenter, but hidden in the Windows XP defragmenter.

These unmovable hidden things are spread across the disk, and were not deleted when the associated files were deleted.

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