Pattern swatches are shifting when exported to PDF and viewed in Preview/GoodReader

I've tried for days to find an answer to this question, but haven't succeeded. Please also be aware that I'm a self-taught Adobe Creative Suite user. I'm working on a Mac with CS6.
I work for a small publisher that produces knitting books. The problem is this: our tech editor has created charts in Illustrator using the pattern swatches feature. (These are knitting charts. Each square contains a pattern swatch representing the knitted stitch.)
I am then placing these charts in their native .ai format into an Indesign file and exporting them to PDF. In Acrobat, the charts look fabulous. In the Mac Preview reader and in GoodReader, the charts do this...
... the pattern swatches shift around inside their squares. Each of those dots should be centered inside their squares. In Preview, when I resize the application frame, the pattern swatches move as I re-size the frame. Any ideas about what might be happening here?
I've tried saving the charts as PDFs and placing those into the InDesign file. Doesn't help. Exporting the charts as images (jpg or tif) works, but I have to make the resolution/file size ridiculously large to get the quality of the vector image. I'd rather place the .ai files into the .indd file if possible.

Try using File>Object>Expand on a copy of the original before making the PDF for placing.

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