If a shop flies the plane they can check it, but that is not a common practice. I usually recommend that a customer comes and plans to spend the better part of a day flying locally, with me or one of my crew usually, to make sure everything is working correctly in flight. On the ground they can run the engine, but usually the CHT's don't get very high unless they do a long ground run. Next time you are at the plane, give me a call at 352-427-0285 and I'll help you check a few of the settings. Otherwise, you need to make sure the probes are wired correctly and installed correctly. If your cowl is open or off, I can help you check that as well. You may want to pull a probe out and put a heat gun on it and make sure the correct sensor is reading. I don't know what it would show, but if they hooked the EGT wires up to the CHT probes and vice versa, they could be erroneous readings, but I don't know if that would show the disparity you are seeing or not.
One easy thing to check is to see if they are reading ambient temperature correctly. If you go out to the plane on a 60-degree F day and they are reading 10F, then there is obviously a problem. You can also compare EGT and CHT temps compared to ambient. If they are both wrong, then it could be a wiring issue like I mentioned before. If the EGT's are correct and CHT's aren't, then it's something else probably. If they are all correct with the engine off, then the probes may not be seated correctly in the cylinders.
Again, give me a call, preferably with your cowl off, and I can help you run through a few diagnostics to see if they are installed, wired and configured correctly.
Full disclosure, I did not install this system for those who may wonder.