There is a very off chance that you're pressing the pedal down slightly when it shifts. If this is the case there isn't anything you can do. The flush won't hurt, it could improve things, but it is really like rolling the dice there. Use the right fluid, improper fluid might cause this. That doesn't mean you gotta get it from the dealer, IIRC Mobil 3309 (http://store.avlube.com/mobilatf3309.html) is correct.

Does this manifest itself regardless of how you drive? If you floor it will the same thing happen or will it shift properly? Also, if you're real light on the throttle (<2500k rpms) same thing?

Check engine mounts too, perhaps it'd be worth talking with the dealer (after the flush) to see what all they can figure out in an hours labor. You'll want them to reset the counter for the tranny fluid, and perhaps the adaptation (the car changes pressure with shifting to 'provide smoother shifting/longer life'). Maybe they can read something with regards to shifting that says its a certain sensor...
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If you're not driving it "like its stolen," are you really driving?