Another clue? I checked the voltage at the battery and at the regulator and they are the same. When I went to check that this time I took the cover off of the regulator and physically pushed the BAT contact closed on the regulator and it started charging at 13+V. This was at a low RPM.
Once I increased the RPM to a driving speed it will stop charging and if you try to push the contacts closed, they will vibrate and will not stay closed anymore.
Also, we have added a dedicate graound wire from the generator to the regulator and from the regulator to the negative terminal at the battery.
Can anyone help on this one?