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Pumps show an animation change, from normal pump to pump with arm when the output is added. However, they won't start pumping out liquid from the train. Note that they will output whatever liquid is in them from before. I tested with all 3 output types: tank, pipe & underground pipe. Behaviour is consistent. Behaviour is also consistent regardless whether item is placed by bot or by hand. Reversing the pump twice resolves the issue. As does sending the train away and letting it come back.

Edit: Removing the locomotive also triggers the pumps.

In the screenshot, the train on the left is not empty because that one functioned correctly and went for another water load after the first emptied into the tanks.

Maybe related: viewtopic.php?f=182&t=49323&p=286147#p286147

Looks like the same issue indeed. I must have goofed when doing my search for pump issues.
On the plus side, mine is pure vanilla and doesn't require a 320MB mods pack

B4SK3 wrote:Looks like the same issue indeed. I must have goofed when doing my search for pump issues.
On the plus side, mine is pure vanilla and doesn't require a 320MB mods pack

Yes this could help for finding the culprit.
I tried it in vanilla but couldn't reproduce it inmy short test setup.

I need backup