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I had a Radon mitigation system installed last week. When I turned on the fan it was all working great. A few days later the pressure level started to drop a little each day, until day 4 it was even. Then when I turn off the fan circuit breaker the level goes negative. So the fan is still pulling.
What would cause the pressure to be greater in the pipe, open to the outside, then in the basement?
You have to get rid of those bubbles, or your manometer will be completely inaccurate. A U-tube manometer works by balancing the weight and pressure on either side of the U. If there's no pressure difference, then the liquid will move until the weights are equal, which happens when the levels are the same (and, if you have the right amount of liquid, it will read "0" on the scale). If there's pressure on one side, it'll push that side down until the weight difference balances the pressure.
This all goes out the window when you have bubbles in the tube; the bubbles add height, but no weight. For example, your center picture shows the liquid tops being equal, but with that big bubble on the right it actually means that the weight on the right side is less, which means that there's more pressure on the right than on the left.
I'd get rid of the bubbles, and then check again.
Just re the bubbles (too long for a comment): If those are air bubbles, I'd think they'd come out with tapping the tube. I had water bubbles in mine. I believe this was due to condensation, with the tube sitting against the cold pipe in a humid basement. If you have condensation around the base of the pipe, this might be your situation.
To get the water bubbles out, I poured the fluid into a dish and sucked the water up with a syringe. (They sell them at drug stores.)
To prevent a repeat, I mounted the tube assembly to a block of wood that was attached to the pipe. Since doing that, no problems.
Was your furnace running at the time? If you have a make up air inlet this will cause the pressure in the home to be positive and push the liquid. It could also be why the values are different check it when the furnace is not running and you may be back to 4 then when the furnace is running close to zero. I have seen this but have limited experience with radon abatement systems. Give this a test and it might explain the differences the good news is even with the furnace running your system is pulling out of the well but the differential pressure has shifted so it looks like it's not working, opening a window or outside door while the furnace is running will also change the differential or that is what I have seen.
I think the tube was kinked. I pulled it out of the meter and didn’t hear any suction. Then while messing with it suction started. Also it rained for 2 days after they installed the system, before I could get the electric on. I think it has water in the meter, not air. I tried to get it out, stuck a wire in it, tapped it, turned it sideways a little. Either way it is working now. Thanks 
fan is still pulling... are you saying that the fan is still on after you turned off the breaker?