I'm using ai files (pdf) in motion which works fine. (fixed resolution is unchecked) BUT: When i'm applying any sort of motion (position, rotation, etc.), it gets slightly cut on the left side of the object. It looks like as the bounding box is cropping the vector graphic.
Move your .pdf out of the group it is in and put it into a new one. It is probably getting cropped because the group it is in is smaller then the canvas size. Putting it into a new group will get it in a group the size of the canvas. Hope this helps.