Why does my pulse command keep screwing up the output?
The pulse command doesn't actually turn on the output for a period of time, it inverts it. So if there is any chance that the pulse event can run when the output is already on (for example, two sequences controlling the same output, even if both are already trying to pulse it), then it's easy for the sense of the output to get reversed.
To avoid this, it is better to use on and off commands separated by the duration of the desired pulse.