Well, I managed to resolve my "missing folder" errors.
What I ended up doing was freeing up some more space on the drive which was giving me these errors (DB had managed to completely fill the drive so that only 4KB was left!) and ran chkdsk on it as instructed to by the DB support team.
I'm not sure why, as there were no errors listed, but after doing that, I was able to repair the pool and all but 13GB was listed as being part of the pool, with no more errors showing up.
I'm still not sure why 13GB was still being listed as being non-pool data though.
But in the end, I was still having problems with a number of applications having incompatibilities with Drive Bender.
Scheduled backups worked, but the non-stop backup feature in Acronis did not, for example.
A couple of other applications refused to create files on the pool for some reason - and creating the pool in the first place changed the permissions on a number of folders to admin-only, which is something I had to fix.
So while I love the idea of having drives pooled together to maximize available free space and potentially speed up disk access, it just didn't work out for me.
At least this time I haven't had the nightmare I went through last time I tried to remove Drive Bender. Other than being left with a handful of empty folders to deal with, restoring my original file structure hasn't been too difficult.