Ok so, it seems that you somehow got a pump that was sneaked behind my mod so it was not aware of the pump. I can see only 2 ways how this could happen:
1. Some of the build events were not handled. I indeed missed one - fixed in 1.0.6
2. One of your mods built or revived the pump but did it silently without raising corresponding events (see parameters raise_built and raise_revive). Unfortunately, I can't help here. If this is the case and you still have the issue in 1.0.6, you can try figuring out which mod does this and ask its author to fix it.
I also exposed a console command /ff.repopulate_pumps - it will check and try to fix any missing pumps. This is not really a solution but may help if you already have a save with a broken state.