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.