Ancient Mariner,
Lots of talk about charging, discharging being the problem, fact is I had a Li battery, fresh from the manufacturer go bang while in storage. Not a big battery, but still. The manufacturer could not explain why.
Of course that can happen if there is a defect (either from manufacturing, as in your case, or from prolonged use, e. g. through formation of dendrites), but it is much rarer than during charge/discharge, and having it happen on a relatively small fleet of aircraft twice within a few days is stretching credibility a bit too far.
So, yes, problems with charge/discharge control seems the best bet right now.
I smell software.
It is very hard to demonstrate software to have an "extremely remote" failure probability, so I read the special conditions for the Li-Ion exemption as requiring an additional (fail-safe) over-temperature and over-voltage cutoff, in case the (software-controlled) battery control system fails.
Bernd