Hello! Glad to hear the issues you ran into were quite minimal (Although the files breaking does sound quite substantial we're glad it was fixed by an easy restart). It would seem that you have gotten all 4 endings then, congratulations!
To break down the AI of Ben a little bit, it is COMEPLETELY dependent on luck. After angering him, there's an around 70% chance that he will spawn with every file transfer you do. After he spawns in one of the vents, he will hang around for about 15-20 seconds, then go away and send a virus onto the main terminal. If you do notice him however, you scare him away, thus preventing the virus. I hope this clears some things up. :)