Two things members have not mentioned so far, first invest in a good hydrometer and check battery specific gravity should be approx 1.280 @ 30 deg C but this will change with battery fluid temp, dont just say my batteries are fully charged check them.
Secondly the regulators fitted to all alternator apart from very old ones are machine sensed not battery sensed. This means that the alternator is being regulated by both the voltage on its output terminal and the temp within the regulator. this not want you want for an ideal charging system, you need to monitor the charge voltage on the battery teminals and the batt temp all this is what a good battery management system does.
Bigboat