Now, if we close all of the valves, the gas in each section doesn't have the weight of the gas above it pushing down (or even the pressure of the atmosphere pushing in). This would mean that the pressure at a lower segment would be higher than the one above it for no reason other than that was it's initial state.
Not true. The air has mass and therefore weight. So small differences in height produce small differences in pressure. We can see this with the formula $P = \rho h g$. For the atmosphere near sea level, $\rho$ is about $1.225 \ \text{kg m}^{-3}$. This means the pressure difference between the top and bottom of a 1m tall chamber is $1.225 \text{kg m}^{-3} \cdot 1\text{m} \cdot 9.8\text{m s}^{-2} = 12\text{Pa}.$
So even with the valves open, allowing the pressure to "equalize", you'll still expect a 12 pascal pressure drop for every meter of height (at least at first). Since this is the same drop that you have initially, there's no movement of air as you open and close the valves.
However, if you block of a section from the air above and below, you've created a closed system which is influenced by gravity, but not the weight of the air above it. So at most, the bottom of the section will be influenced by the height of the section, which is much less than the height of the air above it in the open system.
Depends on what you mean by "influenced". The pressure inside the vessel is the same as it was when the system was closed (assuming the vessel is perfectly rigid and we're not allowing heat transfer).
So you could certainly move the closed system to another altitude and it would have a pressure that differs from the atmosphere at that point. But that didn't seem to be your question.
You were asking if opening the valves where they started would cause air to move. It won't move because even though the section above might not be open to the atmosphere, the pressure inside is the same as the atmosphere at that altitude. Instead of the weight of the atmosphere, the rigidity of the chamber provides the pressure. The pressure at the bottom of the upper vessel is the same as the pressure at the top of the lower one. Therefore there is no pressure difference and the gas will not flow from one to the other.
I think one of the the problems I was having is that at the top of the closed off section, P=ρhg, but since h would be 0, that would imply that P=0 and was messing me up.
In this case $P$ is the increase in pressure due to the mass of the fluid above. At $h=0$, the mass of the fluid doesn't add anything to the pressure. But it doesn't mean the pressure is zero.
Ok, so then what is the formula for pressure of a closed vessel at different heights in a vessel. There needs to be some consistency or else you can rationalize anything.
First, lets imagine pressurizing a vessel in freefall. No weight to worry about. Unless it's very cold or very high pressure, we can get pretty close to the pressure by using the ideal gas law $P = \frac{nRT}{V}$. This pressure is created just by the motion of the molecules inside the vessel.
Now, we can place this vessel inside a gravitational field. If we make the assumption that it's not so big that the density at the top changes dramatically, then the pressure at the top will be just about the same.
But at the bottom, we have the same pressure as the top, plus the added weight of the gas within the vessel. That weight is supported by the bottom of the vessel, so the pressure is increased there.
Now consider a container of air on the ground a meter tall. We can consider the pressure in the vessel in a couple of equivalent ways:
The pressure at the bottom of the vessel is due to the weight of 1m of air in the container, plus the overall pressurization of the vessel to 1atm.
The pressure at the bottom of the vessel is due to the weight of 1m of air in the container, plus the weight of the air above, extending to the edge of the atmosphere.
When the valves are open, the added pressure in the container is directly caused by the column of atmosphere above. When the valves are closed, this connection is broken and the two values can diverge.
If, by closing the valves, you don't have the weight of the gas above the vessel pressing down, then the pressure at the bottom of the vessel should now be less.
Imagine you have a stack of 50 heavy springs. The springs at the bottom are quite compressed due to the weight of the springs above. Now you take a rigid box and slide it so that it exactly holds the bottom spring. If you now take the other springs off the box, the bottom spring doesn't expand, it stays just exactly as compressed. It's being held by the box now, not the other springs.
This is the same situation as your scenario. If the valves are open, the box has no lid. The air pressure is created by the weight of the air above. If the valves are closed, the box has a lid. The air pressure or spring pressure is created by the rigid container. If you move either to a new location, the contents remain at the same internal pressure. If you open the container at a new location, the pressure will equalize to whatever is outside.
Simply closing the valves, or sliding the box on top of the spring doesn't change the pressure. You'd have to compress or expand the container to do that.