well actually. . . .I think the mouse IS inverted when you fly. So you don't want it to be inverted. And, to tell ya the truth, I remember back in the day, I just got used to it, and that is the reason why to this day, all my games I invert the mouse. I have Privateer to thank.
[EDIT]Oh, and unfortunately I am so clueless when it comes to DosBox, or changing settings like that, I cannot help you[/EDIT]