After checking out this site a little more, I'm guessing this question belongs in the DPS forum.
My apologies. I'm just a sports page designer at a newspaper who has next to no digital publishing experience whatsoever but was given the task of creating this PDF/app.
I don't do interactive, so I can't help with that, but I think you do belong here, not DPS, because you are not doing an app (but you may find help over there, anyway, if you've already posted).
Couple of things:
You honestly don't need to export as SWF and then place back into an InDesign file unless you are using the SWF-only features. The main ones that people want to use are Page Turn and Page Curl. Don't use 'em. They are faddish and are seldom used by sophisticated designers. (Similar to a drop shadow. Don't use it.) There are some others for Buttons, so don't use them.
Next, interactive PDF files play fine on computers but are very problematic on tablets.
Next, you might want to pick up my book on Digital Publishing with Adobe InDesign to help you make decisions about interactive documents.
BTW, one more thing, Apple doesn't like it if apps are just conversions of what is obviously just a print document. So your switch to PDF was a good choice. And PDF is NOT a caveman version.
I just realized what all your problems with the PDF are.
In email you are "reading" the file using a built in PDF reader on your computer or tablet that doesn't recognize the SWF content. Same with the tablet and iBooks.
Get rid of that SWF.