I noticed I had to restart the dedicated server in order to get persistent gameobjects to sync. I thought it was something wrong with my code but I now tested the bundled AutoSync-example and it shares the same problem.
This is what you should do to replicate the problem:
1. Create new project with TNET imported.
2. Add "Example AutoJoin" and "Example AutoSync" in Build Settings. Make sure "Example AutoJoin" is top.
3. Check "Run in background" in "Player settings"
4. Run TNServer.exe
5. Build and run the project.
6. Open AutoJoin-scene and play in unity.
7. Everything is working as it should.
8. Stop unity and close the other game window.
9. Build and run.
10. Play in unity.
11. Not syncing anylonger.