I have SHIII / GW3 set up as two versions, normal GW3 and GW3 with the S-Boot mod as a relaxer. I also have two versions of 'straight' SHIII, one normal and the other using the uberboot mod again as a relaxer/ arcade game - nothing like sinking destroyers using 2 big guns!. All run using SHIII commander.
However some odd keeps happening with them.
Taking the normal GW3 as an example. My monitor display is set to 1600 x 1200. When starting SHIII commander, it displays as a window but when SHIII kicks in, that displays as full screen. Exactly as I want it.
Without adding or changing mods, it suddenly changed and SHIII now comes up as a window with 1024 x 768 showing on the title bar. I can't get to revert back. The same thing happened with the vanilla/uberboot version. The other two still run as full screen.

Any body got any ideas?