Final images in a saved .pdf from Illustrator don't look correct

Illustrator Newb:
I'm making a design for a new product that comes in 3 different flavors. So I have 1 design, in 3 different colors. 
I created all of my different parts for the design in Photoshop CS4 as .pdfs and placed them all in an Illustrator file (except for the text and a few shadows, strokes and such). I'm having problems with 1 of my placed images. It's placed 4 different times, and all 4 are either not showing up or are cropped in odd irregular ways. I have no paths or other hidden parts in the file that would cover them and it only shows up wrong when the Illustrator file is saved as a .pdf.
I went back to the original .psd thinking there was a problem w/ it, and resaved it under a new name and it still saves in AI all broken up.
Because I have 3 different flavors, I've done this in the other files, from that same orignal .psd and they turned out fine. And because this design is confidential I can't post pictures of the error to help describe my problem... The problem started yesterday and we're already behind production schedule.
But any help would be nice. Please and thank you!

Also:
The first design I made in AI I saved the .ai file under a different name and changed the minor things I needed to make it the other flavor. I can't go back to that original file because I keep getting a Runtime Error when I open it. Not every file has this error, just the original.. THE ONE I REALLY NEED.

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