Had the same problem. Here is my solution:
My mainlogo ist: logo.png and it is located in: /skin/frontend/default/MYTHEME/images
So I resized the logo.png and uploaded it to: /skin/frontend/default/iphone/images
Every think works fine now!
Notice: It is already a logo.gif in iphone/images/ first I replaced this logo with my resized logo but that didn’t work. Maybe this template is porgrammed to use “logo.png” or it is because my main logo is named “logo.png”.
What ever, it works fine for me.