Most likely because since you changed the screen size, QEMU changed the pixel depth from 15- or 16-bit pixels to 24- or 32-bit pixels and the colors will now be different.
This is most noticeable due to the fact that the square didn't change places. i.e.: If you create a larger screen size, the square will move in relationship to the pixel depth. The square didn't (noticeably) move, so the screen didn't just "zoom in", it actually grew in pixels so the square isn't at the same row/column anymore.
Anyway, we will need more information to be sure.
Ben
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http://www.fysnet.net/the_graphical_user_interface.htm