Checkdisk (GUI) stops prematurely

This may have come up before, but I didn't notice it in the first few pages of the search results.

When I plug my external HDD in at TAFE their network screws it up (permissions?).
As a result (when I'm at home) I have to run chkdsk on my drive or Windows claims that it is "Read only".

When I run chkdsk (from the GUI) it completes the first pass, but it stops on the second pass.
I normally have to run it 3x before it will actually complete the entire sequence.

Of course it always reports that there are no problems with the drive and the HDD functions normally.

This problem doesn't happen if I'm using my VM (i.e. chkdsk works correctly the first time, every time).

I have run sfc /scannow on my system and it doesn't report any errors.

Does anyone have any ideas about how to fix this annoyance?

I reinstalled W7 a few days ago.

That has fixed the problem.