I'm getting a possibly related problem that I haven't seen reported -- or can't find reports of -- here.
In 0.99.5 RC1, iOS SDK 4.2, XCode 3.2.5, writing a project targeted at iPad/iOS 3.2, with Base SDK of iOS 4.2. Project uses the project structure from the XCode templates. The problem is with Code Sense, not compiling. XCode is convinced that I'm writing code for OS X; it won't autocomplete or syntax highlight or jump to any cocos2d/iOS specific features. Instead, it completes OS X specific features. To reiterate, it gives me no complaints on compilation, but it's frustrating to code like this.
When I look at a file with both OSX and iOS code in it, e.g. CCTransition.m line 135-139, it's clear that XCode is touching the code inside the __MAC_OS_X_VERSION_MAX_ALLOWED #ifdef, and not in __IPHONE_OS_VERSION_MAX_ALLOWED.
Any idea how to snap XCode outta this? I've double- and triple-checked my Base SDK, iOS Deployment Target, Targeted Device Family, in all configurations. I've also tried every option for the compiler version. No dice. I know, XCode, you're running on a Mac, that's great. But I'm coding for an iPhone. Yeesh.