I was having this same issue - then your reference to "tick rate" gave me a clue... I had frozen time using commandbook's "/time -l 12pm" command.
As soon as I set the normal time cycle in motion (/time 8am) the pumps started working normally.
Since I like the time to be frozen, I have tried setting the time-lock-delay setting in plugins/CommandBook/config.yml to 200 (default is 20), froze time again, restarted the server and tried it again.
After several hours, the pumps are continuing to work fine.
