I am on Lion - and in the command line, when I open up my project using "subl ." in my project folder - it opens up the last project I had open before I quit Sublime.
I have the Max Preference "Restore windows when quitting" unchecked.
How to I prevent this behaviour? Is there a preference setting for this?
I think the behavior you want can be enabled by changing the hot_exit and remember_open_files settings. If you check out the "Global Settings - Default" preferences, there are some comments there describing these settings.
If you want to change them, you should override them in the "Global Settings - User" file to preserve your changes across updates.