IMO if you're measuring the 12.5V while your MH engine is running, that isn't sufficient for charging purposes. You need a charging voltage >13V. Since you used the "umbilical" cable for the charging current that may be your problem; the wires may be too small and you're suffering voltage drop. I ran a separate 10 gauge wire for my ToadCharge and zip-tied it to the umbilical cable.
First thing to do is check all your connections to make sure that something isn't loose. If that doesn't raise your voltage you may need to consider running a new charging wire.