The file that's different is probably your settings.dat, which is supposed to change in accordance with your settings (your profile and license key, at least).
As to why it would stop loading properly in steam, but load fine outside steam... that's puzzling. Normally I'd figure it had something to do with the steam overlay, but I'm not aware of others having that problem recently (though perhaps there are those that do, and have just switched to running it outside steam).