I noticed this problem when i saw that the stirling engine that was powering a pump was overheating. When I checked i noticed that whenever an update happened near a pump (placing an engine next to it or even redstone updates) it would retract the suction pipes and wouldn't work anymore until i destroyed it and replaced it again.

The same thing but with an engine

The engine is working but the pump isn't pulling fluid:

Test with redstone updates:

Besides buildcraft, I am also running optifine, the ender tanks mod and the multistorage mod. Don't know if this is a bug or something that I caused, so I'm open to suggestions.

Redstone turns off the Pump. This is by design.

The special case with redstone power through an engine is considered a bug and will be fixed. The redstone power going into an engine should not affect the Pump.

Ok, thanks for clearing that up for me :D
Looks like i will have to connect them through a conductive pipe for the time being.

You can also power the engine through a block. Gate -> block -> engine - > Pump. Should work.