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It sounds like your fields are reversed. Does Premiere have a reverse fields option? If not, try moving your AE animation one pixel up or down in Premiere and see if that fixes it.
You probably have reversed the fields and/ or offset the imagery with an odd number of scanlines. as Navarro was suggesting, offseting the content vertically by one scanline/ pixel should re-align the field order. If that doesn't fix it, you have to tippytoe your way thru your projects and look if all your source footage has the correct footage interpretation and that you render with the correct resolutions and field order. Especially the latter could be important when going back to Premiere as it will simply scale any content that does not fit the current project settings, also misaligning your fields. If you are rendering to AVI formats, you may also need to manually interpret files in Premiere as sometimes the correct pixel aspect ratio information and field dominance does not get embedded in the headers.
Are working in PAL or NTSC? The field order is opposite, lower field first in NTSC, upper field in PAL. I don't know how you've set-up your render, but you might want to try rendering progressive full frames, No fields.
Another cause for excessive flickering is when you work with images that have been sharpened, either by hand in Photoshop or sometimes by the digital camera or the scanner used to capture them. I do a lot of animation based on hires photos. Whenever a picture has been sharpened it flickers horribly when animated. If I cannot source an unsharpened image I have to resort to partial blur.