Try again with the flash forum. I was trying to find a link to the one I think fits best when my web pages decided to hang up. Post this link there so they can see what we said:
http://forums.adobe.com/message/5551258#5551258
Adobe Flash Pro Forum:
Ah, well. I sure don't know which of the many forums to pick! Look them over.
http://forums.adobe.com/community/flash
If you post again to the flash forum, post a link back here so we can see what they said.
So my response autosaved from before started like this...
I'd like to convert my Computer into a Space Ship! Maybe we can help each other out... 
What you are missing is that there is no conversion from Encore to an app; and probably no conversion from an Encore style flash player web page to an app.
The Encore to Flash output is not an output to use in any flash program; it is to be used in a web browser using the flash player as an element. It only has a tiny bit of actual flash that might be used within the flash program - the flash player that is imbedded in it.
The flash format compressed (flv/f4b) video files can be used in other apps, but it would be easier to export your files in a format that itunes uses; it doesn't do flash, does it?
It is possible that a person who knows flash could look at the pngs (the files in one of those folders you have that are images of the menu pages) and sort out how to put them/find them in a swf player code, but I suspect that you've got a long way to go.
Is there an adobe program that will make an itunes app? That is where I would start.
That may be the adobe digital publishing app:
http://help.adobe.com/en_US/ppcompdoc/Step_by_step_guide_to_dps_se.pdf