I happened to reboot for another reason, and tried opening subl-- and it worked properly. Then I quit ST2 and tried again, and it spawned 2 windows like everyone else in this thread experienced. So- is the issue at hand really ST2 not completely closing? Is there a stuck process, so when subl is activated, it opens an additional window and focuses on both? I looked using ps -A but didn't see anything running. Is there a flag not set or something that lets ST2 know that is has truly closed?