Hi Gral,
Well, good news and bad. The good news is that I have got it working! The bad is that I'm not entirely sure how.
I just thought I'd give it another go tonight and see what happened, it simply worked.
The only thing I have updated today is to the latest, 10.8 version of the Xcode dev suite so I can only assume that there was some library contained in there that I was missing? or Xcode is required for it to run, which seems unlikely.
Anyway, if It's of any help here is the command line it produces to run:
"/Users/Alex/Desktop/FGx.app/Contents/MacOS/fgfs"
--callsign=G-AVYX
--geometry=1280x800
--enable-fullscreen
--disable-splash-screen
--aircraft=c172p
--airport=KLVK
--fg-root=/Users/Alex/Desktop/FGx.app/Contents/Resources/fgx-fgdata
--fg-scenery=/Users/Alex/Desktop/FGx.app/Contents/Resources/fgx-fgdata/Scenery
Hardly a complex one I'd say? I had tried with fullscreen disabled, splash enabled and a selection of airports and aircraft.
At least it's fixed now, but I wish I could be more use as to why.
If there's anything else I can do to help let me know.
Alex