Had same exact problem...mine turned out to be the security feature. Trying to tune it(superchips tuner) while the battery was not fully charged screwed it all up. After charging battery, removing certain fuses and tuning...it started up like nothing ever happened...reinstalled fuses and it. Went thru about 10 days of hell. Thanks to the superchips tech(an awesome young lady...got me thru it.
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Alsalsa
2003 Adventure package: Air Suspension: 20 inch wheels w/BF Goodrich LT 325 60R20 All Terrain T/A M+S: Flowmaster exhaust: Airaid cold air filter: Superchips flashpaq: Pioneer AVIC-D3 w/Navi, Ipod and 12" dropdown screen: Rear Camera: Jet Chips Air Mass Meter: Remote Starter: Cognito Kit: Third seat