Interesting. As you suspected, eh? (I was on the phone w/Tom when this happened, actually ). Well, it could be worse. The fact that you CAN use the standard charger at all, even if you have to double charge, is still a pretty cool bonus. Given the change of chemistry, I remember that we were doubting that the stock charger would even terminate charge properly. So I wouldn't say we "failed". Not entirely anyway.
It may be possible to mod the circuitry to have a different time out. I know on the MAX712/713 chips, this is set by tying two pins to certain other pins on the chip, or even leaving one or more of them open. This is obviously not ideal, not a "drop-in" solution, but still. If it were easy to do, we could do a bunch of them at once, and this *probably* wouldn't hurt with standard B90 packs, as the detection would shut off fast charge at the appropriate time--although we would want to test this to make sure.
Anyway, those are my thoughts, FWIW.