Images imported in illustrator not showing when saving work as pdf

Hi, I'm new to illustrator and have encountered a seemingly strange problem.  I'm trying to create a figure for a scientific article consisting of a plot (.pdf, created in Mathematica) with another graphic (.pdf, also created in Mathematica).  I've imported the two files into illustrator cs6, making sure that they are within the artboard margins.  They look fine there.  However, when I save the file as a pdf (to be used in subsequent applications), and view it (either in Preview (on mac) or in Acrobat Reader), the second graphic doesn't show up.  Any ideas?  Thanks in advance.

Thanks for your response.  It doesn't seem to matter which layer is higher in the stack.  I also checked that each layer was set to "print".  I think the problem is on the Mathematica side --- the problem I have arises with pdf graphics generated in Mathematica 8, but not in 9.  Hmm.

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