Default session does not open.

My saved default session only opens when I quite the app from OS x's dock and not from pressing the x in the upper left hand corner. May be trivial but once closed in the normal fashion, I have to recreate my default session from scratch. Saved sessions also don't reopen if closed in this fashion. Its very easy to forget to close the program in the "odd" manner that it seems to require (from the dock and not from the red x in the upper corner of screen). I had the same problem with macsword and it led to me not using it. Can't find anything online that comments on this problem. Please help!!!