So my cars an 850 AWD manual, with the 2.4L LPT. I bought an ECU from another 2.4 LPT automatic and had it chipped.

In the whole time ive owned the car, with my OEM ECU i've hardly ever got any CEL's except an o2 sensor or if I forgot to plug my MAF.

With this ECU, i have the transmission codes (normal)
and misfire codes, evap codes..

The car runs great, with both ECU's

What could cause these codes, or my OEM ecu to not display these codes?

 

Who did you have tune the ECU? Perhaps they did a poor job of it.

 

some local guy, i'm sure he didnt do the best of job. I know when I first bought the second ECU it had a check engine, but I never checked the codes, i figured they were transmission codes.

It might just be that, probably some generic tune causing these codes.