Question did you charge up the new battery first before you put it in? You charged it later off the bike so that is good. It sounds like you did the correct thing in changing batteries. Why do you think the new battery is not charging now? Once a battery is full the voltage regulator will reduce the voltage so as to not over charge. From what you describe the regulator seems to be working properly.
So a fully charged rested battery will read @12.7v. 3/4 full @ 12.5v. 11.5v fully discharged.
The regulator needs to put in a higher voltage to charge up to 14.3 V. As the battery gets full it will drop to a lower voltage.
If the charging seems to be erratic I would check for poor ground connections.