The last batch of "fixed" phones that have caught on fire have not even been in use. The last few caught fire during the night when hooked up to a charger. They seem to be catching fire around 4 - 5 AM, which assuming the phone was plugged in at midnight of before, should be after the battery is fully charged. So at first blush it would seem the batteries are being overcharged. However, the phone that caught on fire on the airplane was apparently not in use or plugged in. In fact he said he had turned it off and then the fire began.
My hunch is the batteries are being damaged during the charging process, and once that occurs it's just a ticking time bomb before the layers in the battery come into contact and cause a big exothermic chemical reaction. Often it happens right away, but sometimes not until some other physical factor triggers it.
The original batteries that Samsung thought were the problem probably weren't manufactured quite as well, and thus they simply manifested the overcharging problem more easily. The other manufacturer's batteries in the "fixed" phones have slightly better manufacturing, and thus they can simply stand up to the overcharging abuse a bit better, and since it didn't manifest in Samsung's testing, they assumed it was purely a problem with the other batteries.