Hmm. Now you have me puzzled. A google search came up with the following from MSDN:

http://social.msdn.microsoft.com/Forums/en-US/sqlintegrationservices/thread/94cc1c91-f699-481a-be91-703a912b0f2b/

Hopefully this approach will help. Haven't ever gotten to the point where the window won't recover from the right click/variables method but it sounds like the next step may be to try the window layout refresh.