that solved part of the issue - it looks like the other part was my own dumb fault..
I was loading an extension from a folder with a dep file, but without the extensions quoted in the dep file - i.e. $ tce-load /mnt/sda1/source/buildtc/08_10_25/wireless_tools.tcel
/mnt/sda1/source/buildtc/08_10_25/wireless_tools.tcel
tar: can't open '/mnt/sda1/source/buildtc/08_10_25/wireless-2.6.26.tcem': No such file or directory
Note that it seems that once there has been an error like the above, then "tce-load /path-to-file/wireless-2.6.26.tcem" does not work. On moving wireless_tools.tcel to a folder without the dep file and after re-boot, things again work fine.
On a different subject, it's difficult to be sure, but it looks like "tc checkfs pause" or "tc checkfs" or "tc base norestore checkfs" do not run the fs check - the re-boot part does however run.
Edit: would it be better to use e2fsck maybe?
Edit2: I just ran fsck manually - since the fs had been mounted a bunch of times, fsck ran for some considerable time so it definately did not run on boot with "tc checkfs"