This is the way I see it happening: So humans make FTL, and they have super advanced computers (The absolute lowest was x64) then, a cyberterrorist group let loose a computer virus, but it was only designed to infect x64 and above. Computers that were infected became 'breeding grounds' for the virus which replicated across the modern internet, until there were no x64+ computers left in existence. Then people started making older versions, the DCPU-16 and the TR-3200. The story makes sense, because computer viruses are real, and there are no discrepancies that I can see. It would also be cool to have derelict spaceships, with computers that don't work but can be salvaged for parts. (Unless the virus heated up the computer until vital components melted, that would be hard to salvage. It is possible, it happened to my old computer, it got so hot that the hard drive broke.)
I am from the future... of the past.