Make sure you haven't accidentally reversed the charger leads during the battery swaps. The only way a battery can "reverse polarity" is if it was fully discharged and charged back in reverse. It's very rare that that occurred, but still needs to be checked since you did in fact return a reversed battery. I'd guess the battery that reads 11V after a little use is good and doing all the work while the 3V battery is being charged backwards and being destroyed. If my wild guess is true, eventually, the 3V battery will get to 0V and reverse polarity too.
Once you figure it out please share the findings.