Epic post.
Right, ok, I seeeeeeeeeee. I apologise Hoppy... seem's you're right. I thought, with the camera in manual mode and the FEC altered, you wouldn't get a preflash, but seem's you do :| Very annoying.
My other flash (YN460), which has also been playing up, has a setting on it which take's into account the pre-flash, so it seem's. But I have been using my Infrared trigger mainly so never come across this problem before.
So basically: I cannot use my onboard flash as a Master flash, you are correct Hoppy and Pete. And the gel situation must just be a weird thing where it's altering the light amount somehow. Solution: fix my Infrared trigger.
Thank you guys! So much appreciated, learnt something tonight!