Well, this has become my standard suggestion by now - have you tried disabling GUS sound (in dosbox.conf set gus=false)?
And make sure you have selected Soundblaster Pro @ IRQ 7. Strike Commander works fine for me (floppy disc version, though).

Hey I got the sound to work. I've transferred the game to an older Desktop that has an actual gaming joystick port. Fortunately, your suggestion for the sound worked, but nothing I Seem to do makes the joystick work. Either the in game calibration has no effect (And the cursor just flies around) or it says "Joystick calibration not correct".

Its an older type of joystick, I had no luck using a newer Sidewinder type joystick (in the game the joystick could be used as the mouse, for cursor and even for VIEWING in the game itself, but it could not FLY the plane)..

Any help there?

Strike Commander had that kind of problems on real hardware, too (at least on my system, i had to constantly calibrate the joystick). Try changing the "timed" parameter in dosbox.conf and/or setting a fixed number of cycles before starting the game.

Do you mean this:?(About cycles?)
core=auto
cycles=auto
cycleup=500
cycledown=20

or did you mean put a fixed number in the timed
joysticktype=auto
timed=false----------<?
autofire=false
swap34=false
buttonwrap=true

What cycle count would you recommend?

Also-
I had a different version of SC (think the floppy one) and I used the keyboard to fly and it worked good. I Got my hands on the CD version and when I try and fly the plane in the cockpit view the plane goes what direction I want it to, but the direction arrows ALSO control the view in the cockpit, so I cant see what i am doing because it keeps moving the view around when I try and move the plane. Its really annoying. (Which is why I opted for the old game port style joystick I Have, plugged into the desktop with a joystick port on the sound card)

Is there anyway to remap the keys?

You should take a look at the DOSBox readme and the .conf file, which has example settings.

If you have a "digital" Windows joystick (i.e., a modern one), you should use it. I haven't used a gameport joystick in ages, but i remember having to recalibrate very, very often. You won't have that problem with a USB joystick/joypad. Every controller supported by Windows should work in DOSBox.

Before trying to use the other joystick I WAS using a modern Joystick, a Microsoft Sidewinder Force Feedback 2. And in the game it DID work for controlling the cursor in the menus and talking to people, and even in flight I could use one of the buttons and the joystick to look around, but the actual joystick wasnt working when it came to controlling the flight of the aircraft.

So obviously its compatible, and it works with some parts of the game, but not the actual flying.

You need to use Alt-O and set Panning Control to something other than keyboard if you want to use keys to fly.

I have the same problem with the joystick.

I used a an old Gravis and my newer Sidewinder, but even after re-calibrating it just spins around.