What the difference in configs ?
Project with Branches Tab:

Project without Branches Tab:

If you only have one branch specified in the VCS config, you won't see a Branches tab.
TeamCity doesn't show branches in a project in case it knows nothing about them, i.e. there are no builds/changes in the project since project have been created. So if there is an old project with builds, newly created one has no knowledge regarding those builds. Try running a build in a branch, it should help.
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