The neg wire output from the solar controller has to go to the Trimetric shunt same as all the other negatives, for the Tri to "read" that. It sounds like you have that wire going to the neg battery post and not via the shunt.
You will find the output amps as shown on the controller display can be higher than what is on the Tri, when the battery is nearly full and you have a light on, eg. The battery might be accepting 3 amps and the controller says 6 amps, which means the light is using 3 amps.
The Tri only shows what is actually going into the battery.