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I run duel 2003 250 evinrudes. My port "check engine light" comes on when I first start up. It goes off after a few minutes ( I presume when the engine has warmed up) and does not come back on again untill next trip on a cold start. I have replaced the water filter. Any help would be greatly appreciated.
If the engine runs well otherwise and you have determined that it is not water in the fuel I wouldn't get very excited about this. It is likely that the computer is sensing a low battery voltage on initial start up and this is triggering the light. You might want to check all battery connections and have the battery for that engine checked to see if it has a weak cell. If you have a battery parallel switch try starting the port engine on ALL and see if the problem still occurs.
Other possibilities are a temp sensor that is out of whack or possiby a glitch in the guage itself. Next time you are near a dealer it would be a good idea to have the codes in the engine checked to verify what is causing you problem
Watch the light to see if it flashes in a pattern. My Suzuki did that and the pattern was flash-pause three flashes-- 13, so I called the dealer, told him the code and he told me the cause and what to do about it.