your last sentence is exactly correct... but that doesn't mean tossing batteries, just keep the weaker ones for use with other weak ones when longevity is not required.
next time you get vastly different readings when removing cells could you take notice of which cell was lower in voltage?
from reading that thread i linked in my previous post i noticed that the cell closest to the atty was normally higher in voltage (atleast when inserted with positive terminals pointing toward head of flashlight)....
which brings to mind another good tip i've read here and on other forums--- always put batteries in the device with positive terminals (with vent holes) pointed away from the atomizer. (not much of a saftey tip especially if your PV is sealed, but if using a home made mod which way would you want the gas to vent?)
my thoughts would be to try to match batteries that discharge quicker with cells of similar characteristics. maybe save two of those lower reading cells, charge them and try using them as a pair. the main thing is to try to match batts inorder to prevent reverse charging.
short of buying a ZTS tester (or whatever it was called) there is no way to accurately determine the state of a LI battery and even this type of tester relies on an IC to compare the readings of the battery being tested to a database of readings of batteries of known status. (sounded kinda like voodoo when reading at CPF).