I have a large set of data (about nine million files of various sizes and types; mostly student home directories) and when I run chkdsk on the volume it spends a long time on a particular index. By "a long time" I mean several hours, a substantial fraction of the total time the chkdsk takes. During most of the chkdsk you can see progress every second, but at a particular index number it just stops. If I do a chkdsk again (without any changes to the data) it stops at the same number.
I've moved the data from one volume to a newly formatted one, and the same thing happens there. As I delete chunks of the data, the chkdsk time becomes shorter, but there is still a single index that takes a sizable fraction of the total time right up to the point where the disk is nearly empty. The index number in question changes sometimes when I delete a chunk of data.
Is this normal behaviour? Can anyone explain it? Is there a special index that contains all files, or something along those lines?