I was having issue with the sound stuttering on the intro/startup, and when doing things like switching to different seats, and holding the fuel buttons when fuelling up before a mission.

I didn't see a fix, but figured one out for myself, and just wanted to share it in case others have similar issues.

Short Version:
Set DosBox to run the graphics in Overlay mode.

Long Version:
Navigate to the games root directory; Megafortress/GameData
In each of the 4 conf files (Megafortress, _Editor, _SkyMaster, _SledgeHammer, edit the line:
output= ... to
output=overlay
Save the file

Hope this helps somebody/anybody.