I am sorry but I can't imagine there being any link between charging and failure of the mic.
Most people won't wait for the device to be charged before playing with it, nor should they.
If 90% of people don't wait before use and 2% of people have a failed mic there is a pretty good chance that the 2% of people with failures didn't charge their device, it does not prove a link.
I would have thought looking at whether the mic is properly detected with correct drivers loaded would be a good first step.
I would also say that if plugging in an external mic works then you have proved to some extent that the software is fine. I would guess that it might be a hardware problem. It may be a batch of microphone were used that were bad and that final pass out testing did not cover checking the microphone (quite likely I would have thought).

Perhaps if you can post up your serial numbers then someone at the factory can work out what hardware was put in these.