A possible explanation is that the system had not been properly cleaned and so there was added friction from a residue inside the syringes. And then when you ran it, it was flushed out. I would rule out firmware. First because the command to take a stroke is a single command, so there is no way to corrupt it and create a pause at half stroke. Second because faulty firmware will not be corrected through a power cycle.
You should get the upgrade at least anyway, because it will need it sooner or later