Some PDF files garbled in Safari and PDF HD

I have a 3 page sample of a book on my website (generated from InDesign) that reads fine on the Mac Safari and other programs on the Mac.
However, the PDF will only show garbled, overlying text when viewed on the iPad Safari and PDF HD. It is not file size related as I have an 8-page newsletter nearly four times the size of file and also created in InDesign --> PDF that views just fine.
I have exported the PDF and also print to PDF as a new file and it still comes out a mess.
The graphics and music illustrations are ok, some lines of text, and titles. The fonts used are Times TT and Helvetica. There is also a IPA linguistic font used. Basically all other text in the three pages is just garbage.
Anyone else see this happening and how can I fix the situation so clients can see the sample on iPad? Can the imbedded EPS files in the document be what is fouling things up? The illustrations are essential for the sample from the book.

I have this same problem in all PDF readers and Safari.
The problem exacerbates itself when a PDF document gets zoomed in or out.
I have some large, multi-page PDFs that are fine and some that aren't.
I even have one or two page PDFs that exhibit the same issues.
I can't see any pattern to whether a PDF will view correctly or not.
I have reported this via Apple iPad feedback.
You may want to do the same to let Apple know tis is an issue on some iPads or iOS software.
Here's the feedback link
http://www.apple.com/feedback/ipad.html

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