First, that's an awfully big image to be using to create a time-lapse video unless you plan to pan and scan or severely crop. Second, what version of AE? Third, what happens if you take the scale at the bottom of Camera Raw and change it to fit or reduce it below the about 22% it is now showing.
A better workflow would be to bach process your original images scaling them to a suitable size for video production, then import as an image sequence in AE.
If your AE and Camera Raw are up to date you should have no problems.
I think the bach process workflow is what I need to do.
AE, Camera Raw and photoshop are all up to date though. I wonder if this is happening because the resolution of the raw images are huge....
This doesn't happen to my t3i Raw images. Only happens to 5Dm3.
What software do you recommend for bach processing? Lightroom?
I'm guessing that you cropped in camera and when you shoot RAW the crop is honored but can be removed. I would use Lightroom. Set up a preset that resets the crop and process all of the frames and then export a png or if you want to do some advanced color correcting in AE, select any of the 32 bit image formats and render your resized images to a specific folder. Then import the images as an image sequence in Premiere Pro or AE and do the rest of the work. Importing an image at a time into AE and sequencing the layers in nuts...IMHO
One other thing, before you shoot any more images with this camera go through the menu and reset it to not crop your images.