ClearCase creates version 0 when you create an element (or a branch), which is usually checked out automatically. Version 0 is always either empty, or same as the branched version, as you noted. There shouldn't be any problem simply checking in version 1 on top of it.
Note that branches are created when you check out, not when you check in, so you shouldn't get any warnings on check-in. If you post the exact command line and warnings/errors, we'll probably be able to help you out more.
It could perhaps be that you've created a new element on your branch, and you're missing "/main/0 -mkbranch" in your config spec.
HTH.
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