Couple of days ago I had the issue with the pipes when being next to each other will connect after a chunk reload.
Well now that I am using the colored pipes I have the opposite issue. The same color pipes are disconnecting on chunk reload.
For a second time I see that these exact 2 pipes are disconnected, however this time there was a third spot as well.
The first time I connected them again and waited to see if it will happen again.

The blue pipe on the left should be connected to give water to all my boilers (2 bronze, 2 steel, 1 large). I am using 1 bronze water pump for this.
The white pipe on the right is my pipe coming out of the large boiler.
The bug seems to happen after every server restart.

Here are some more pictures. The last one is on the chunk border.