Ok, so your fridge is the load you're checking, and it's 12v and connected via a DC-DC converter to step down from a 24v battery?
I don't quite have straight in my mind (w/o a diagram) your component placement, but a couple of comments:
1) perhaps the shunt and meter are mismatched (some meters can be adjusted in the settings, e.g. for 100, 200, or 300 amp shunts). The shunt probably has its specs stamped on it, and the meter has to be set to match it. A meter set for 100a, but using a 300a shunt, would give you low readings.
2) if you put the shunt between the battery and the DC-DC converter (not after it), the result will be slightly more accurate because it will include the converter's losses as well as the load's draw. If you want to compare the DC load amps to the total amps from the battery, that's the best place to put it. However, like Brewman said, it also matters where the SCC is connected to the circuit (at least in daylight).
Your last sentence is interesting - can you sketch the circuit you have (no masterpiece expected), and snap a picture?