Update: I've now been able to (once) capture a zero second sub using the sequencer, so I'm not sure if the exposure length is related.
I've also found that if I leave it long enough, I will eventually (after about 8mins) get a message informing me of the camera timeout.
I found the logs, and have attached one, which will hopefully aid in debugging the issue.
sg_logfile_20160611094738.txt (70.7 KB)