HDD not writing to old pagefile.sys areas

[Darlis]

You're welcome. Take a look at the How do I defragment "C:\$Extend\$UsnJrnl:$J:$DATA"? FAQ entry on how to get rid of the UsnJournal (temporarily). But you can count on on Windows that it will write new files next to the (frequently accessed) system files again. 

[rp1915]

I decided to clear as many of the oddly placed system files as I safely could, so I emptied the prefetch folder and used fsutil to delete the usn journal, as suggested. I then used chkdsk /f and forced a process idle tasks to rebuild both (I know it will take a while to properly repopulate prefetch) and found that chkdsk then reported that $bitmap was corrupt and incorrectly listing free clusters as allocated.

Why none of these errors came up before I don't know; I suspect the errors in $bitmap were behind the problem all along. I've gone through several iterations of chkdsk /f until it ceased to report any errors and then run Mydefrag and now have a disk that looks perfect again. I'll give it a while to rebuild all the prefetch data and then run a 'monthly' script to get back to full performance.