ClearCase creates version 0 when creating an item (or branch), which is usually automatically extracted. Version 0 is always either empty or the same as the forked version, as you noted. There shouldn't be any problems just checking in version 1 on top of it.
Please note that branches are created during verification, and not during registration, so you should not receive any warnings during registration. If you post the exact command line and warnings / errors, we can probably help you.
You may have created a new item in your branch and you are missing the "/ main / 0 -mkbranch" in the configuration specification.
NTN.
source share