I just tried it, just out of curiosity, because otherwise I don't think there's any point in using the Cobra for the job of getting people off Titan.
But I noticed that weird thing you described - in my first (failed) attempt, the TG Pulse Neutralizer charged incredibly slowly, something like 3 times slower than normal, even with 4 PIPS in SYS. And the next time I managed to pass and it worked normally.
In both cases I activated it in time, and in both cases the decontamination limpet was active, because Cobra does not have enough utility slots for caustic sink.
So maybe it's some bug, I'm not sure.