I have never had any problem opening Scenario files with Sqedit or map files with Sqsub in ToD.
Are you patched up to date? If not you can get the latest patch 1.06
here (I doubt that just patching it will fix the problem but you need to make sure you are patched up to date anyway)
Once you are fully patched, and if it
still doesn't work then I think I would uninstall ToD and then reinstall it. (and then patch it again!
)
I would be prepared to put money on a reinstall solving the problem for you.