If and how long a thesis parked on a restricted server will be indexed by Google?
There are several reasons for not showing up in your Scholar profile. Depending on the configuration of your university repository, maybe Google can not access and index the document, just as Ian pointed out. However, even if it is online and available for anyone to see, Google can be blocked (robots.txt) or still have not index those pages. 

So, all you can do is wait for Google to index (without any defined time to do so), or add your thesis to other repository or even to a personal website (if your university allows you to do so).