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Just an FYI - I just spent my afternoon tracking this down and wanted to share it in case anyone else is getting stuck!
I leave the "window size" debugger on pretty much all the way through development, but found that it can cause performance issues on the iPhone (tested on 3 and 4). I think that vertical scrolling in the iPhone trips the window.resize function (because of the way the top address bar disappears as you scroll down) and I was getting tons of freezing and stuttering and awfulness on what was otherwise a very simple page.
Once I turned off that checkbox everything was totally fine again (and I have used it before w/o any issues) so it's certainly not a problem to fix, but is a good thing to be aware of when tracking down performance issues!