In my case there was no black hole machine, no engine damage (I'm pretty sure, anyway)... ships just acted straight up WEIRD in that system. Some would do the slow down and stop forever thing, some would act totally normal, and I had one or two groups that ran up to a wormhole as though they were going to enter, and just squatted there in an un-AI-like way - they obviously intended to go through.
From what Chris said (x4000 IS chris, right?), my guess is that on some level some of the ships were waiting in odd situations for ghosts that they didn't recognize were dead, possibly as a result of a serious overload of turrets and shields and fighting in that system, or as a result of my updating to .16 right in the middle of all that madness.
But whatever, I'll leave it to the experts.
Which save do you want on mantis? I assume the first save after the first frozen ships... but I'm anal and keep 5-minute autosaves, so you're welcome to any of those weird scenarios I mentioned.