Offline/Missing Image Sequences in After Effects CS6 with Color Bars

I am working on a stop motion animation in After Effects CS6.  Each clip has been imported as an image sequence from stills on my hard drive.  When I open up After Effects, all image sequences now have color bars over them, as if they are offline.  Trying to reload them does nothing.  I cannot 'link media' because it isn't just one file; it's an image sequence so there are many of them. 
I first noticed this when the color bars appeared in my dynamically linked comps inside of Premiere Pro.  Everything played smoothly the first time I opened the project in Premiere CS6, after originating in CS5.5.  Then the second time I opened up Premiere, the color bars appeared on the linked comps.  I hadn't yet opened up my AE project in CS6 yet, so when I did, AE converted the project and I resaved it. 
Any help related to this issue would be greatly appreciated. 
Mid-2009 Macbook Pro
Mac OS X Mountain Lion
8GB RAM
Adobe Creative Suite Production Premium CS6 w/Creative Cloud

Thanks everyone, I think I'm beginning to solve this.
Rick, thanks for your advice.  I tried this and it worked.  The reason I didn't do this before is that, because it is stop motion, I couldn't remember how many frames I had imported for each sequence.  For instance, if I shot 54 images and only imported 52 into the sequence, I wouldn't remember which 52 images to import...this might still be causing a problem, but I don't know yet.  I think in most cases I imported all the images in a folder, so the image sequences should be fine.
I am having another problem, however.  Even though the issue seems to be fixed in AE, it doesn't seem to be fixed in Premiere...each image sequence is dynamically linked from AE, but each dynamically linked comp is still being show with color bars as they did in AE...I think that maybe my Premiere project is still linking to the old CS5.5 AE project, and not the new one opened and saved in CS6...

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