It's likely that your live battery was dropping to about 2.8 volts under vaping load, and the other was dropping to cut off (about 2.5 volts), stopping you from vaping any more. Not a good thing to vape to cutoff, but sometimes it just happens

In your case, the mismatch wasn't that much. It really wasn't 3.4 Vs zero.
That what I had figured; that they weren't that far off in voltage so it wasn't too bad. It was really only a problem with the 14500s I was using in a 5V regulated mod. The good thing about a regulated mod is you get the same vape as long as your batteries hold out; the bad thing is you get no warning in the vape before your batteries die. The 14500s were not enough to get me through a whole day.
Two 18650s in series in a regulated mod (VV this time) not only last me all day, they last me two full days of fairly heavy vaping with two or three hours to spare. I did run them all the way down a couple of time just to see how long they'd last and got similar results; now I just use them for two days and swap them out for another pair while they charge.
Anyway, they point I really wanted to make is that the whole point of keeping batteries in pairs; buying them in pairs, using them in pairs, charging them in pairs, storing them in pairs and not mixing batteries in pairs; is to try and have your two batteries in as near identical condition as possible. Two batteries that age together should keep close to the same internal resistance as they age. When one of the batteries starts to behave differently than the other, say taking longer to charge, then they may be starting to differ from one another enough to where it may be cause for concern. I feel that any time your batteries start to change in performance, either longer charge time, shorter vape time, getting warmer than they used to, then it's time to start thinking about new batteries.
Having said all that, it could be the charger. There's a good thread on using your multi-meter over on the CandlePower forum that also discusses how to check your charger. I just prefer to err on the side of caution when it comes to Li-Ion bateries.