Let us deal with the ‘Subscribed’ button and popup at the top of the page first. This is not to show you what topics you are subscribed to. This is a visual notice of when new posts have been made to topics you subscribe to that you have not yet viewed. So when it is zero that simply means there are none at the moment.
Not seeing subscribed topics in your Simple:Press profile form is, however, rather odd considering that you DO get the subscription emails so there are definitely successfully subscribed topics. I have not encountered this behaviour before.
Can we discount caching or are you using a WordPress cache plugin of some kind?