Okay so here's what I did.
I made an extra backup of my FF disc, Used PowerIso to change the video files for the first two logos. The first being Eidos, the second being Square. I have a nicely remade Eidos to add in and a custom Team Avalanche/SquareSoft/Square Enix one to put in. I added the Team Avalanche and Square Enix to the sqlogo.avi, and that one plays fine. I replaced the Eidos one, and it skips over it. I've tested the video in WMP and it's a perfectly good AVI. Am I missing a key factor here? Is there a command or problem that would prompt FF7 to skip that video without me pressing start/esc.
Help appreciated, Thanks