I have several resources in my iPhone app and when they get compiled they all get added to the root of the resources folder in the app regardless of the Xcode grouping struc
My problem is that Xcode is not noticing and new or changed files within those folders and hence when I build my project, none of the new or changed images are in the target app's resources.
This is a long-standing bug; it's bitten me many times while working on Adium. Please file it in RadarWeb. And thanks for the reminder; I've filed my own bug report as x-radar://problem/7232149 (visible to the public in OpenRadar). You should mention this bug number in your own bug report.
As a workaround, you can right-click on the folder reference and choose “Touch” to tell Xcode that the folder has changed.