Was it deleting the FS9.cfg file and having FS9 rebuild a new one that resolved it?
Yes, deleting the old CFG worked. Just incase you're interested, here's a part of the old cfg. I can't find anything out of the ordinary here, but then again I'm not very good with these sorts of things

[STARTUP]
DEMO=0
LOADSIM=1
LOADWINDOW=1
SHOW_OPENING_SCREEN=1
STARTUP_DEMO=
[GRAPHICS]
FULL_SCREEN=1
PERFORMANCE_MODE=0
DEF_PERF_MODE=7
TEXT_SCROLL=1
AUTO_LOD=0
DETAIL_TEXTURE=2
WATER_EFFECTS=1
TERRAIN_USE_VECTOR_MAP=1
TERRAIN_USE_VECTOR_OBJECTS=1
EFFECTS_QUALITY=1
GROUND_SHADOWS=0
SMOOTH_VIEW=1
IMAGE_SMOOTHING=1
TEXTURE_MAX_LOAD=1024
COCKPIT_HIGH_LOD=1
AIRCRAFT_SHADOWS=1
LANDING_LIGHTS=1
IMAGE_QUALITY=0
TEXTURE_BLDG=1
TEXTURE_GND=1
TEXTURE_WATER=1
AIRCRAFT_TEXTURE=2
SEE_SELF=1
TEXTURE_QUALITY=3
LOD_TARGET_FPS=28
NUM_LIGHTS=6
Thanks again for the help
Vulcan1