This should be fixed now. Let me know if you have any problems in the future!
Update: Found the cause of the "problem". It's not actually a bug. When you go to My Updates, by default it shows you replies to your posts AND new content on anything you favorited.
In other words, if you favorite a user, you will see posts by that user in the updates. If you favorite a tag, you'll see all questions with that tag. If you want only replies to you, click the button at the top labelled My content.