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When the check engine light comes on the PCM detects an emissions related fault and stores a fault code. This code will need to be read with a scan tool. It can be as simple as a faulty gas cap but of course can be more severe. I recommend you try another pepboys or autozone as they will usually scan for these codes at no charge. Once you have the fault code number let me know what it is. It will be a P followed by four digits. For example P0401. Do not authorize any repairs until you reply back with the code number.
I'm sure they did scan for the codes and nothing came up and they did it at N/C. That's why I'm confused. Is it that hard for the scanners to pick up problems?