C:\Games\FreeSpace2\fred2_open_3_6_9.exe -fredhtl -jpgtga -mod mod\StarTrek
The -mod flag looks for a folder in C:\Games\FreeSpace2. So it was looking for a folder called StarTrek and failing to find it.
I think we may need to pop up a warning when mod folders aren't found rather than silently carrying on.
meh love you lots, worked a treat, now for a simple two fighter mission set around DS9

Mission one,
On a routine fly by of DS9 with some high ranking star fleet officers on board, to access the station and look for any structural damage following a tractor beam miss hap that has left the station without weapons,
A Ferengi shuttle warps in, and hails DS9 and asks for assistance,
moments later, 2 Klingon birds of pray warp in demanding that the "traitor" is wanted by them for duping them out of some, 100 gold plated latinum bars, and say that any interference from star fleet, will be meet with violence, DS9 in response tells the Klingon's that they would be violating Bajoran space if they do so, the Klingon's then say something in Klingon and end comm's and start firing on the Ferengi shuttle, at this point you are asked by DS9 to engage the target,
If the ferengi shuttle is destroyed you fail the mission
If you defeat the two birds of pray, you complete the mission and the story continues
If you go AWOL you are demoted and transferred to the far reaches star-fleet to make tea for scientist's
Well that's if for my first simple campaign, it has every thing in it to help me learn Fred (for now anyway) and I'm sure i'm going to get stuck lots of time and have loads of head scratching moments
But thank you Karajorma for helping me, it was very much appreciated