I also faced this issue today with latest version of this mod (and it's dependencies). I'm using a ton of other mods, but AFAIK none of those touch the pumps. The closest other mod might be flow-control. Anyway, I did the disable + re-enable pumps mod trick and replaced the pumps manually. Luckily I only have pumps in three places, so it was not so hard to do. If you want more information for degugging this, let me know!
EDIT: My savegame was started before the last update. I'm not sure about the timing of the problematic pumps with mod update. Is it possible that the "left-overs" were present in the map before the update and they are still there?