As per Trips, you need to put a trickle charger on the battery during extended storage (or disconnect the battery). The ECM draws some power to keep its memory refreshed and will eventually drain the battery. IIRC, the radio also draws some current to maintain the presets.
If you weren't maintaining the battery charge, that's probably your problem. There is a good chance that you have ruined the battery.
If you disconnect the battery, the engine will run rough for a while until the ECM relearns engine params. And you'll have to reprogram radio presets. And you won't be able to pass an emissions test until you go through several drive cycles.
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