Good information there, Wpz2000
I knew about the chip/circuit inside the batteries (or at least the OEM batteries). Some of the cheap, 3rd-party batteries do not include this voltage and temperature sensing/reporting circuitry and when Froyo/2.2 was released, folks with these wonky batteries discovered that Moto had changed the kernel to prevent a battery that does not contain this voltage and temperature circuitry from being charged.
Also, I do believe that recovery (or at least custom recovery) runs a minimalist kernel that can charge the battery, albeit slowly. But when you are only in bootloader mode, the kernel is, of course, not running and the battery will not be charged.
I didn't know about the upper and lower limits you mentioned, so that's excellent info. to know.
I wonder if wiping the battery stats would help (I don't think these are auto-wiped with CWM since there's a separate option for that). SBF'ing should take care of "resetting" any battery stats or kernel settings, so if the OP reverts to Froyo/2.2, that might