Explain why a 24v system that runs off of 4 batteries which includes a 12v feed- that's powered by two of the batteries are getting no charge from the alternator.. the other two are charged well.?

With the batteries in series, the alternator provides the same current, and therefore the same charge to all the batteries. The alternator can take no account of any current being drawn from the 12V take off point. Part of the charge current is being fed to the 12V load and not to the batteries. Therefore, the 12-24V batteries are being fully charged while the 0-12V batteries are being partially charged. Over a period of time, the difference between the charge levels will become more obvious.