Premiere and AE are obviously processing the effect differently. Well, as you know, whatever works :)
...unless these are shots BEFORE the effect processing, in which case, welcome to the wonderful world of codec management. They're not all as bad as Quicktime, where no two applications handle the same material the same way, but every one of them makes a case for frame sequences. :) Personally, I use .exr for all my work, converted from .dpx or .cin scans. When ripping DVDs/Blu-Rays, I immediately convert them to frame sequences in .exr or .png (if 8-bit) for processing.
_Mike