compltaset77, no the holes don't have to line up. just lightly tighten the atty, as over-tightening it will cause the short you are experiencing. throw out the
batteries that have over-discharged, and only pair those batteries that routinely stay above 2.5V, hold the nominal voltage of 3.2V for the bulk of the cycle, and come off the charger at 3.6V. there must have been a short, because
typically when vaping the batteries won't drop much below 3V, if that,, before the vapor trails off and you feel the need to switch batteries/ recharge.
edit: i'm thinking more about 3.7V batteries. the lifepo4, can end up around 2.5V and even lower before the vapor trails off. you don't want to go too far beyond this though and it's good to check the batteries with a meter when you feel the vapor trailing off to get an idea as to what the voltage actually is. the lifepo4 batteries can take a lot of abuse, and routinely bounce back from heavy discharges without any ill effects, but having any that read 1.1V should definitely go in the trash.
again, i think it's the atomizer that caused the short, but you'll want fresh batteries at this point and you'll want to know how long or at what stage of vapor production and performance your batteries reach a safe discharge level before needing to be recharged. then you'll have an idea as to when to replace them and you'll have a much better chance of getting the same performance out of them recharge after recharge.