You did not mention them so I assume you have no panels or wind generator. Your battery charger is putting 13.4V into your batteries and the voltage reading at the controller is over 17V.
There is something wrong with your batteries if your voltage is that high.
That said...you misunderstand your manual I think.
The controller/compressor you have will work at either 12V or 24V ...
From the frigoboat manual:
A supply voltage of either 12 or 24 volts dc is required. The controller will run from either voltage without any special settings or adjustments, switching automatically to 24v mode if the voltage is above 17v.
Protection is provided for the following:
(1) Low voltage. To prevent the batteries from being totally discharged, the compressor will be stopped if the voltage at the terminals on the controller falls below 10.6 volts (23.4 on a 24v system). It will not re-start until the voltage rises above 11.7 volts (24.0 on a 24v system).
(2) High voltage. If the voltage exceeds 17v, the controller stops the compressor and switches into 24v mode, but will not attempt to start the compressor until the voltage reaches 24v.