I'm with 007. Consider checking the actual charge volts directly from the battery terminals. If the batteries are actually charging, as they should, you'll need to determine where in the measurement (not charging but measurement) circuit something has broken. If the batteries are not charging, then you are looking in the charging circuit for where the volts are being lost.
I do not think the problem is with the transfer switch. The TS deals with only 120 VAC. If the inverter/charger has 120 VAC incoming and the outbound volts are not correct, the inverter/charger may be suspect.
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