Thanks for the help, I'll look into my own files when I get home.
One interesting thing I noticed this weekend while playing, was sometimes when I CREATE my own scenario, changing nothing but generating a world and changing AI starting units and such, when I start the game up sometimes it's s different version.
It's been years since I was familiar with the changes in each version, but I loaded a custom scenario once and there was no trebuchets (for some reason this also broke the upgrade chain of my catapults once I wanted to upgrade to artillery even though I had all necessary techs and resources) and then I replayed the game and this time I had access to trebuchets. The tech tree was also strange in some games, as there would be missing techs on the tree but the arrows leading to them were still there (ex: fascism is one I remember, the arrow pointing to it was there but fascism itself was missing). Sometimes radio was removed completely and the arrow did correctly display to advanced flight whenever this happened.
Tl;dr: steam version is definitely buggy and weird.
Edit: I have windows 8, if that makes any difference.