I think that something wrong with windows size saving.

Let's take an experiment:
1. Open, for example, firefox on display 1;
2. Set it's window state to normal (not maximized) with not to much width and height. Remember its size and position;
3. Now maximize it's window;
4. Press mouse wheel on window caption to move it to the next display;
5. OK. Now if we restore window state to normal, it's width and height are equal to screens client width and client height, not like they were when we open firefox.

DF Pro v3.1.8.109 (Beta 9).

This is a known issue that was said be be unresolvable, however I believe that just recently there may have been a workaround put up on the forums that Jon is looking into.