I have the exact same problem, which was described in this topic Re: Mouse pointer does not move below 25 line in the 50-lines text mode. (SOLVED)

Which comes down to this: when playing Master Of Orion, I cannot use mouse pointer completely freely, with transitions between DOSBox in windowed mode and the rest of the screen. It's either a choice between being able to use the pointer without restriction inside the window [when it is locked with CTRL+F10]; or being able to access also for example Windows Taskbar without the need to use ALT+TAB, but at the same time not being able to go down to the bottom of window [unless I press CTRL+F10]

It was happening on my previous system [which was Windows XP] and is happening on the new one [which is Windows 7]

In the aforementioned topic there were some solutions, but apparently way over my head. That 8x12_50 program does not seem to work, I don not know where to put this bios_screen_size.diff file, I also do not have that mouse.ccp on my drive ready for possible modification. Could someone please give a step-by-step instructions for people like me, who use DOSBox something like every other 2-3 years, just to play some old game?