Deletions returning errors

We've just installed SQL Source Control 3.8.17.115 on our 2012 server. When we attempt to delete a table and commit changes, every single time we get Error: CheckIn returned with ChangeSet ID=0, nothing to Check in? Didn't expect 0 actual 0

Is there anything we can do to fix this? We tried unattaching and reattaching. We tried unattaching and then deleting the files from TFS, then reattaching. If we're unable to delete objects, source control is useless to us.
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