no, i don't have that, nor wine windows, kde windows, gtk windows, java windows
no, i can't replicate
have you verified if you leave them maximized and the windows are set to remember the size?
in the windows in question, click on the icon, it will call the window menu, there open advanced/special window settings
if there is not the option you need(first tab) is in the configure window behavior
remember that if you are using compiz, this can affect how windows behaves and you need the compiz manager to edit that