HDR Time Lapse .mov flicker problems

Using Lightroom 2.3 trying to create an HDR Time Lapse .mov with quicktimepro. I have slight shutter adjustments (flickers) to correct in many images. I was unable to use manual exposure as time was an issue so auto exp. and manual focus was my only option. This was a scene over water of an amusement park and the waves are crashing, which I did not think of, so the ocean highlights created in camera slight speed adjustments...
Is there a way to match the sky exposure evenly in all the frames (240 of them) using an auto batch eye dropper action in Lightroom or PS3?
To add to my problem I have a single jpeg and need to convert to an HDR using Photomatix. I know raw would of been easier but was not thinking....
I have already tried to tweak each image seperately so I am half way there but still have flickers. Can anyone offer advice that won't take me all day.
Thanks for your help....
David

Thanks Sean,
I was hoping lightroom or PS3 could batch correct the exposures to match each other....Jao gave me "match total exposures" from the settings menu and this helped but still have to correct some by eye. You are right about the shutter drift. I used a Nikon D200 and that has issues. Looking to buy the D700 soon.
My other problem was the HDR conversion of a single Raw frame.....I am going to try and "match total exposures" before doing the HDR and see if that works....

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