We made the same experience, and what we know so far (hopefully we'll find a solution!) is that APPLE does not allow to load any "active" content, i.e. SWF pages with AS3 code. Even a stop() seems to be treated as such!
Very disappointing, but on the other hand not that surprising when you know a bit about Apple's business practices.
On Android it looks more promising...
We can get into more detail by PM or email. As you know Apple forces everybody who signs the contracts to become an iOS developer to only talk positive in public...
Perhaps we find a way together to overcome those hurdles and can use interactive content on iPad also; but in the meanwhile I am skeptical