This ships fate is fairly straight forward. At some point during her voyage, life support (and presumably auxiliary support as well) suffered a critical failure, killing all her inhabitants.
That's not the mystery here as I see it. This ship is different from the other generation ships that I've studied. It has no biospheres at all, yet in the first log, when the computer is doing a systems check, it clearly states " +++BIOSPHERE+++SYSTEMS NORMAL+++".
How is that? How is the ships computer recognizing a system that is not present on this ship as being online? Perhaps that's a clue to the answer. These ships almost certainly had to have backup life support systems. While it is known not a lot of oversight went into their construction, as is evident by the fact others discovered report mechanical failure due to design flaws as well, it seems unlikely both would fail simultaneously in tandem. Unless there is a glitch in the main computer, or a virus of some sort that is. That may explain why it's recognizing a biosphere that it doesn't have, and why the emergency a.i. was only able to attain 92% human capacity.
That mystery aside, what else is remarkable about this ship is the lack of biospheres like the others, which is compensated for with extra holding tanks. It has a large external cargo rack, bigfer than some of the others, to carry more planetside supplies. The lack of biospheres is interesting. Does that indicate this ship was a very basic model, and the low cost may have played a role in the critical failure of its life support and the apparently malfunctioning computer?
Back in ancient times, before WW3, humans on earth used wheeled vehicles that ran on combustion engines utilizing petroleum fuel. The quality of those vehicles could vary, depending on the price you paid for them. Some lasted longer than others, some would experience catastrophic failure very soon after purchase. It seems to be a quality problem that has plagued mankind's earlier engineering feats and I suspect that is the case with Achlys as well.
You get what you pay for, folks.