I think the problem might be that you have the bottles connected to the same output tube.
To begin with, pressure at the bottom of each bottle is created equal to the depth of fluid in each bottle.
If the bottles contain different depths of fluid or if one is higher than the other, it will try to run from the higher level one into the lower until the fluid surfaces are equal. (This is how the Romans used to set 2 points at equal level by using a tube and some water). Because the tops are sealed so no air can get in, they will not be able to achieve this but there will be
some transfer of fluid from the higher to the lower bottle.
Presumably the output tubing you have employed is very narrow so viscosity and surface tension will slow this down and you might not notice it happening.
Because the tops are sealed, the fluids will also tend to drop out of the tubes until enough has run out to create a partial vacuum over the tops of the bottles. This will stop when the weight of fluid equals the external air pressure and take longer if you are using flexible bottles which can cave in slightly as the internal pressure drops.
Unless you use very narrow tubes so that surface tension stops air from getting up the output tubes, this vacuum will draw air in to replace lost fluid and it will just keep leaking. To prevent this, use long output tubes which go up until they are higher than the tops of the bottles then curve back down again. In this case, all dispensing will be by air pressure only and might stop when the bottles are nearly empty if the pressure is insufficient.
When you start the pump, the vacuum in the selected bottle vanishes and the pressure at the bottom of that bottle is now the weight of fluid plus the applied pressure and this forces the fluid down the tube down into the glass. Unfortunately, this same pressure is now also present at the base of the
other bottle since they are connected. Because the air pump is quite powerful, the combined pressure will probably be greater than the weight of fluid alone in the other bottle and the selected fluid is forced into the bottom of that bottle and pushes the other fluid up out of the top (as well as tending to mix them together).
Solution? Just keep the two output tubes separate!
Keeping the air input air tubing at the highest point of each bottle will avoid any tendency for fluids to flow up the tubing towards the air switch and gum it up.
If you are using an output tube so narrow that there is no leakage, you might not even need the air pump. Just keep the tube straight down from the bottom of each bottle and the weight of fluid will force it out once you open the top of the bottle (using the switch) and destroy the vacuum. Slower and not nearly so controllable though.
I have attached two suggested layouts depending on whether you want the containers vertical or horizontal
) I'm having trouble with the pump tfor the milk. You can see here in the picture: http://www.ge.tt/#!/8sMJAa7/v/0
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