it's simply a bug (that will probably never get fixed?)http://code.google.com/p/arduino/issues/detail?id=78All the code to save and restore the windowsize (and last sketch) is already in the IDE, a patch was posted on the devlopers mailing list, but somehow nobody cares to fix this.
It's a pain in the rear
probably never get fixed...nobody cares
these kind of things happen with projects with volunteers
f you always remember to close with ctrl-q it will remember your window size and position
I am using Windows
For what it's worth, if you always remember to close with ctrl-q it will remember your window size and position for multiple windows.