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I think I can solve this.
I used to have a problematic Subaru Outback XT. When I would disconnect the battery to clear the codes, the same thing would happen, it would take a long time to start.
I asked a few forums why, and a guy came back with something to the effect of "the ECU is running a systems check to make sure everything is still there. It had indicated a no power situation"
If you could, disconnect the battery and reconnect it like you usually do, then when you go to start the car, switch the key to the ON position for about 10-20 seconds, then try and start it. Let us know what happens.
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