Hi Joeren,
I don't think you have done anything wrong. We have had the same issues, but intermittently and I am having a hard time nailing down the exact use case to consistently reproduce the bug. We have also had cases of the flip side happening - on repository connect, the synchronization dialog tells us there are local changes yet when we try to check in, the check in gets cancelled because the repository and library are the same. It is happening right now with an extension file that I am sharing via the library.
Anyway ..... I have come to the conclusion it is a bug and not something you are doing wrong.
Regards
Bruce