I have written about team alerts issues found in TFS 2012
Here are some updates
1. Since TFS 2013, the issue of ignoring “preferred email” and using AD settings is fixed.
You can choose your preferred email and it will be used for sending team alerts
2. New issue since 2013 update 2: if team alert IS NOT included in contributors, alerts will not be sent – read here. fix/workaround – just include the team in Contributors group