The iPhone will kill applications that are consuming too much memory. If your embedded web view has a lot going on (this could be huge images, video, etc.) then you are at risk for your app being killed by the system. In general, reducing complexity can help. You can also try unchecking 'Use WebKit graphics acceleration" in Hype's Document Inspector; sometimes this can change the memory characteristics of animations.
Safari has new memory tools that can often help: