We had similar issues with the Jangaroo version of Open Flash Chart on the iPad when showing several charts on one page.
The underlying problem is that in the current setup, each JooFlash "plugin" is a heavy-weight iframe with all the JooFlash code (850k of JavaScript!) in it, over and over again!
This would be comparable to the FlashPlayer plugin being installed many times, with no runtime code sharing whatsoever.
To get this working reliably on a device with low resources (CPU, memory), we need to let one JooFlash render several stages. In theory, JooFlash is already capable of doing so (this part of the code is inspired by DartFlash, thanks guys!), but I never tried it out. You would only load JooFlash once, and then create several stages instead of one. Note that these can be anywhere on the page, they are <div>s referenced by their id. Putting a JooFlash application into an iframe is not necessary, it is only more convenient to completely separate JavaScript and CSS from the main page. If you let JooFlash render everything into one canvas (cacheAsBitmap), there is not much CSS involved, so for a single application like ChessFlash, it should work. However, you have to be careful with static variables / singletons, which in the current implementation would be shared between stages.
If that sounds too experimental to you, the pragmatic solution is to split multiple views to multiple pages for the mobile / iPad version of the Web site.
Greetings
-Frank-