This has been a problem here for a long time. BWS will sit there for a while before closing after a script runs, even if using manual intervention (file/exit) to close it.
Win server 2012 r2, BWS 11.1 patch 6 (Build 1833)
It's not so much of an issue on another box running windows server 2008, but defnitely an issue on Win Server 2012.
