I think I may have just had this "non-charging" battery issue myself.
I have had the controller off the wall mount today testing and binding a new DT92E, normally it is always left on the wall mount.
When I had finished I noticed that the battery was about "half full" on the indicator, (it had been off the mount for some time) however when I put it back on the wall mount I noticed that the battery symbol went away completely - which normally only happens if the battery is 100% charged. If the battery is not fully charged it normally changes to a battery symbol with a lightning bolt through it when replaced on the wall mount.
Although it may have only been a glitch in the display of the icon, I suspect my battery was not charging...
I remembered the suggestions you made here and tried them, but they didn't work.
Parting the batteries while powered on did not display a battery with a cross through it, only the time. Also when I allowed the batteries to reconnect it still stayed with only the time and no battery charging symbol.
What finally did work for me was to shut the unit down completely - removing both battery and external power, then applying
only mains power to let it boot up, after booting up I inserted the second battery and now I have the proper battery charging symbol, and the charging symbol returns each time I put it back on the dock, while the battery is not yet fully charged.
If I shut the unit down and then started it up on battery power then applied external power after it booted it did
not show a charging symbol. I had to boot up with only external power and then add the battery after booting.
At no point did I ever see battery with a cross symbol through it appear - even now if I part the batteries I don't see such a symbol.
Just though I would pass this technique on for anyone who might be having trouble getting their battery to charge, as it appears there is a bug in the charging logic of the unit that can cause it to believe the battery does not need charging when it does.
First time it has happened to me in 6 months use though.