All of the bugs for this has been resolved, so I am making a new one. When I was building a bubble column near a skeleton spawner the soulsand would switch between working and not working. I would do nothing and the bubbles would turn off. I stood still for 20 minutes and the bubbles stop pushing up skeletons and start with me doing nothing. 

Here is what was around it: i had a string on a lever to activate a piston that pushes the Skelton into the should be bubble column