Last time I did that, the system kinda shorted or something when I reconnected it, for some reason. Or at least it acted very very funny when I attempted to start it up again. As in, it didn't want to do anything at all. And it freaked me out that it was cracklin' and crap when I put it back on the post, but nothing was on in the car.
well after you disconnect the battery, your computer has to "relearn" things like the ideal idle speed and things like that. after 30 seconds of running at idle it should be fine.