Hey Massi,
The problem with the skins is likely due to you running an unreleased version. We have changed a few things with the Site Settings page that did cause issues with the unreleased 2.8.0.3 version. Your best bet is going to be to compare the theme.skin from the packaged framework skin with the skins you're running. Anything having to do with the Site Settings page should definitely match the new framework theme.skin.
We are aware of the 2.9 version not showing up properly. This was a packaging issue and we've resolved it in an upcoming release. I'll send this release to you directly so you can test it in your environment.
We're not able to reproduce the Google.protobuf issue. Do you have any "pro" modules installed? Only the mysql version uses Google.protobuf but it could have been packaged with the mssql version at some point in the past so you may have it. In that case, you should be able to just delete it.