[chris powell]"is there a way for after effects to save the sequence in the same variable sizes that i imported them in ? "
Sorry, no. AE expects to see images in a sequence as the same exact size. You have to think of image sequences as one-to-one substitutes for movies.
If you imported a Quicktime movie, would you expect AE to react well to successive frames of 640x480, 720x486, 1440x1080, 1280x720 and 720x576? Do you even think quicktime would allow you to make a movie like that?
It's time for Plan B to do what you seek to accomplish. You'll have to do a lot of "Save Frame As" commands in AE, or work in Photoshop.
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