Hi Kevin,
Thanks but that doesn't sound like it's the problem I'm having. A particular pulse sequence I have trouble with is just 5 pi-pulses of the same speed between energy levels with a tlist of length 1000, meaning that each pulse takes place over around 200 time steps so I don't think pulses being too short is a problem.
The oddest thing, which I should have mentioned in my opening post, is that the conditions for this failure to happen are all over the place. Sometimes it depends on which state I begin the simulation with, sometimes it's the strength or presence of any collapse operators, sometimes it works if I just add some "dead time" to the end of the tlist.
I can't make head or tail of it.