I am seeing something similar to viewtopic.php?p=3427#p3427
but I see it when I create a rounded list with prev and next buttons at the bottom. The list fits fine in the designer - but when I run it on the iPhone 4 the list takes up more space and pushes the button off the screen. I've fixed it by using a scrolling panel for the list and anchoring the buttons to the bottom. But - it does show me that the layout does not reflect what actually happens on the iPhone 4 - I'm sure due to scaling issues. If it were possible to preview "as an iPhone 3GS or as an iPhone 4" - that would be nice. I found simulators on the web that helped me see what the generated code looks like on a 3GS.
I suggest having an option to hide the footer toolbar as well. I think you have the code in there but they still show when using the browser - if there is a way around that - it would help. They disappear when I create an icon on the home page and run from there.
I do run into the files not being regenerated bug fairly often that I mentioned earlier- not sure what is the cause of it.