@drewbullen – the proof of concept project we are using here is unfortunately pretty complex. We are using also some other HTML5 contents made with other packages, so not only Hype. Anyhow i was able to track down the problem a bit. The Hype scene that is causing the problem is a demo scene from the Hype showcase gallery (Lake Nakuru Responsive Page). The page is using an animated symbol (a little pulsing dot). When i throw out this symbol from the scene the problems are gone. Apparently this symbol is somehow persistent, even when we load/unload the Hype scene in the Ionic carousel… We will give a try again this week and see if we can do a better solution there. I am thinking about detecting some custom Ionic events and using something similar in Hype like described in this Baker related article here: Embedding within the Baker Framework: Ebooks for the iPad
@Daniel - thanks again for taking the time mate! 
Cheers!
Sandor