Did you dis-connect the ECU before charging the battery or use a "spike "protector when you charged it ? Im sure you will be more lucky than me but ....if you jump or charge these things with the ecu connected it can , and Does fry the chips , ive had this before with a huge misfire after re-charging a battery on a racecar and found a Drop out on the chip that needed replacing to cure it .!
sure its only a blocked filter or something stupid tho .