This is reproducible 99% of the time on Mac OS X Snow Leopard. Using the experimental terminal window, after creating a connection, closing it will create one of two issues. 

If the connection has been closed behind the scenes due to timeout, closing the terminal tab for that connection will freeze netbeans for several minutes. If the connection is still open, netbeans will completely lockup and will not come back. I cannot access menus, only get the spinning cursor until I force quit.

The only work around is to never close a tab and only open new connections. It isn't exactly a work-around more of avoiding the problem altogether, but basically the application does not gracefully handle closing of terminal window tabs at all.