Adopt the latest PDF 2.0 specification
Flash-based PDF interactive output from InDesign is, to be kind, rather problematic. Flash-based interactivity is problematic with mobile-based PDF readers, including Adobe Reader on the iOS and Android platforms.
Please do what you can to adopt the PDF 2.0 standard promptly. Like a lot of other users working with interactive features within PDFs, I'm hopeful that by creating conforming documents, rather than hoping for conforming PDF writer and reader applications with widely varying degrees of success, would help InDesign take advantage of intrinsic security and interactive capabilities of the PDF 2.0 specification.