I booted to maintenance and ran chkdsk on all the disks. Then I ran ifx /fv and save the log file. Then I did a normal boot. What I notice is that ifx checks 3 drive but there are actually many more. C D E F G H K U are on the system and working.
This log was created while you were booted up on C: - is that your main system or the maintenance partition? The results are only meaningful if you were booted from the system that's having problems (each installation has its own set of INIs).
As to the drives listed... The system on your C: drive has references to files and directories on C:, D:, and F:. If you've never created a program object or shadow that refers to a file on, say, K:, or have never repositioned a folder window for a directory on K:, or renamed a file on K:, etc., etc., then you might not have any references to K: But... given that you have over 9000 handles for just 3 drives, that seems improbable.
Normally, I don't recommend CleanIni because it's far too aggressive, but in this case it may be called for. It will delete every handle which isn't being used by a program object or shadow. If you have 9000 handles now, you'll end up with fewer than 1000 when it's done. Overall, it's a lot safer for the non-technical user than XFix which can do irreparable harm if you're not up to speed on this stuff.