CO2īs(every gas) density depends on temperature !
I would say that your "readings" of CO2 concentrations in the hives are
an indication of the ventilation from buttom to top(the only kind) that you
mention.
Meaning that your hives are ventilated - good.
In cases where the air(+ gases) are stale meaning that no ventilation
is taking place the CO2 would fall to the buttom of hives this happens
due to a higher density of CO2 than air when they both have the same
temperature.
CO2 is leaving the bees at a higher temperature than the surrounding air
has, due to the
draft in the hive and the lower density(due to the higher temperature)much
of this CO2 is
drawn out at the top rather than falling out the bottom as could be
expected.
Conclusion : you may have found a way to determin ventilation levels in
behives
Arnie