Have you tried changing the video settings for Dosbox?
If not, try opening dosboxMOO2.conf with notepad in the game's directory and set the following:
My Master of Orion 2 just now started going automatically from full screen, non-windowed (my preferred viewing method) to 640x480 in a DOSBox window. Hitting Alt-Enter gets the full screen back for a second or so, and then DOSBox changes right back to the windowed version. I switched the configuration in the dosbox configuration file to those listed above (they were all different before) and the same thing still happened.
I have no idea what changed, as I've played over 100 hours on my laptop and never had this issue before. Anyone have any ideas on what's going on?