Rendering changes clip timing.

Hello,
I created a project a year ago in a previous version of FCP. I got FCS2 and upgraded all my media applications. I finished the project i am working on. I was watching the dvd when i noticed some weird things. I fixed those mistakes and while i was at it, i tightened up a particular camera angle (camera b's 16:9 isn't quite 16). As soon as i did anything to camera b clips that caused them to need a render they would time shift.
Everything looks fine until a full render and all those clips are timeshifted about a second or two.
I have done all the render clearing/new project/sequence and all that jazz and it is persistant. I have thus far resolved to remove anything that makes the clips render and am now thinking of creating an inferior product. I do not want to do this.
I have searched the forums for about two hours now and have come up with nothing useful. Does anyone have better information, or a few more things i can try to troubleshoot? Time to sleep. Any help is much appreciated.
Thanks,
K

sounds weird and i dont have an immediate solution
however i'd suggest exporting one of those offending clip instances as a self contained quicktime movie (prior to adding filters, scale, distortion or whatever) then reimport that new clip and use it in place of the original instance in the timeline ... add filters etc, then test to see if this new clip maintains its clip timing (it should, especially if you didn't add handles!)
if it works correctly then do the same for the other offending clip instances

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