Battery not charging, but no battery light illuminated on the dash. Battery will take and hold charge from charger. I suspected battery monitoring system. Checked all wires and connections, have continuity on cable from alternator to battery positive. Taken out negative cable with bms sensor and replaced with standard cable just to test. Battery at 12.58v but nothing coming from alternator. Could it be bms or alternator at fault?.

If you unplug the Smartcharge plug on the alternator, it should default to about 13.5v. If it still doesn't provide any charge then it is the alternator at fault. But very odd that it's not triggering a warning at all.