Sorry to Hijack this thread but i seem to have some problems with resolutions changing too. I have an App and the GUI is made for the iPhone 5 but has to be used for iPhone 4 and 3GS too. Now it scales the height but not the width 
UIRoot settings:
Automatic = off
Manual Height = 1136
Minimum Height = 480
Maximum Height = 1136
I still don't have 100% concrete answers on this, after watching too many videos, reading too many forum posts, trying ratioFix scripts, etc....
so lets try a simple q&a...
say you use one atlas for all resolutions...you design your UI at a "middle ground" resolution., for this example lets say..720x1280 (portrait)
we have three variables and a tick box to muck with
automatic off (seems to be what most folks want for this problem)
manual height = ? (the height of the original ui design resolution? 1280 in this example?)
min height = ? (the minimum targeted device height?)
max height = ? (the maximum targeted device height?)
should you adjust manual height at runtime when the resolution height is not 1280? (the original ui design height).
should you only adjust manual height to match the original UI design (if you had SD/HD atlas...you'd change the manual height when you change atlas?)