I think this is related to this post.
I am on Mac OS X 10.8.5 and have a 2nd external monitor and running ST3 build 3059 (stable channel).
The issue I am seeing is that if I have previously closed all ST3 windows/projects and quit ST3. Then when I restart, I am getting a new document created that is on the main laptop display and extends way into the secondary monitor.
If I have a file/project open and quit ST3, when I restart it is opened in the previous location & size. The issue is the new windows on startup are opening in a new location, but with the same size. Can I control this behavior?
I suppose what would be ideal is if the window opened in the location of the last document/file/project and the same size.