The game seems to think my throttle stick is on back to front. If I wanted full throttle on any other game (say, for example, FreeSpace 2) Pushing the throttle away from me would increase the speed and vies versa.
In Dark Star One, it does the opposite. Pushing the throttle away from me, slows me down and vies versa.
It's damn confusing to come off the game and go to IL-2 and wonder why my plane slows down on full power until my brain remembers it isn't playing Dark Star.
I might not of looked through the options long and hard, but I haven't seen any obvious option to sort this out.
Will I need to do something to the throttle it self?

Unlikely. There should be a reverse throttle axis. I don't have it installed at the moment so I can't offer more than that sorry.
Karl

I reinstalled the game.
I don't have a throttle that I use with this game but there is a possible solution.
Under options there is a "Reverse Axis". The default for Throttle is Z-Axis so select the "Z" checkbox under to the right of "Reverse Axis"
Hopefully this will work :)
Karl

when you enable using joysticks and go to the controls menu to adjust the buttons, the throttle should show up as Z axis. For me, there are two spaces for alternate keys but the right one is blank. If you click on that blank space it should say 'reverse axis' when you hover. It'll make a little noise but won't do anything else to tell you it worked (it confused me at first... my pitch and roll were reversed as well, REALLY confusing to fly). The throttle should then work correctly...