I find it incredibly nostalgic that you used to browse the old Outbreak forums on GameFAQs. I also had an account and was active on that forum, along with other Outbreak related forums at the time. Time really does fly by. LOL
There's many players that play both versions. File #2 is more popular because the game has improved gameplay, character balance + improvements, less exploits overall, extra game modes, and more depth to the scenarios.