Opened a different IDML.
1) Noticed that any linked graphics that did not have a file type appendage would not show. Had to go to the actual file, add the appendage, then Replace in the RM.
2) A couple of graphics (AI files) were imported within Picture Frames, but there are no Frame controls showing, so cannot modify the image using those controls. All other graphics using a picture frame do have controls, so looks like it's just the AI file types.
This file also created the mystery 1x1 graphic items (2 of them).