Intake causing CEL problems

I have a cold air intake system in my car which is causing the CEL to come on. Codes read P0440 P 0441 & P0446. I just got back from the mechanic however(a well trusted one) and told me there was no leak as the codes would indicate. The problem is that stock computer is analyzing the flow of air pressure to be greater than what its programmed for. So the issue here is more than 3 codes during motor vehicle inspection wont pass(unless i replace with the stock intake). Is there something available or other option i dont know about?! what if a new chip like a uni-chip was installed to change the parameters. would a short ram intake be any better?

If it helps this is what i have installed in my 03 toyota matrix.
Cold Air system
DC 4-1 Header
Skunk 2 racing cat back

These codes should have absolutely nothing to do with your CAI:
P0440 = Evaporative Emission Control System Malfunction
P0441 = Evaporative Emission Control System Incorrect Purge Flow
P0446 = Evaporative Emission Control System Vent Control Circuit Malfunction

1) Check your gas cap. If it's loose or it's internal check valve is stuck, you will loose positive pressure on the tank and set PO44X codes
2) Vac line, power connector to the purge solenoid is loose or the solenoid is shot (rare). Check the evap system sticker/schematic under the hood for solenoid location.
3) Auto techs cannot/ do not know everything, but you might want to shop around after this diag.

Joel

Check for a disconnected or mis-placed vacuum line -- make sure that any vacuum hoses you removed to install the CAI are replaced on the right side of the throttle body or it will cause the Evap system to throw codes.

i have had the CAI installed since May of this year. About after a month or so was when the CEL came on. I'll make sure to try to vacuum lines. I also got a new seal for the gas cap but im going to try a whole new gas cap if nothing else works. ill let you guys know the update.