I've posted this same question on Stack Overflow here: http://stackoverflow.com/questions/23573916/mobile-safari-ckeditor-cursor-moves-out-of-text-area-when-typing
Basically, when I run my application within an iframe on Mobile Safari, I get some unexpected behavior when I type. If the CKEDITOR text area is in view and I start a new work or hit the spacebar then the view shifts so that I can't see the text that I'm typing and the cursor moves to the top of my iframe. Has anyone seen this before?
work-around: use divarea plugin
So by switching to use the divarea I'm able to work-around this issue. From my testing and the one response I've gotten on Stack Overflow, I'm pretty confident that the cause is using the stock CKEDITOR within an iframe on the iPad. By switching the edit region to a div via the divarea plugin things look great.