I have found the following significant irritations when using Managmenent studio source control:

1. It creates 'connection objects' in the project, these can be very confusing and dangerous as they can easily point to your live environment. This means when you open a script in source control you have to carefully check which environment, management studio has decided to open a connection to.

2. It doesn't sort scripts in alphabetical order?? The fact this feature is missing is extremely aggrevating and is surely very easy to develop.

3. Getting source safe to create the desired folder structure, is impossible (and if not impossible very difficult). Not sure if this is management studio's fault as VSS is