When I build my project (any project, really - I tried creating a new empty project with the same results), it builds fine with GCC 4.2 under either Xcode4 or Xcode 3.2.4.
Might be a bug in Xcode 3.2.4 or the SDK configuration.
Try placing a line like one of these in your Build Settings Preprocessor Macros:
-D__IPHONE_OS_VERSION_MIN_REQUIRED=040100
or
-D__IPHONE_OS_VERSION_MIN_REQUIRED=030103
Without violating NDA (Xcode 4 is prerelease software), I recommend you read this thread in the Apple Developer Forums.
It sounds to me like your installation is borked.
When you installed Xcode4 did you make sure to install it to a completely separate directory to your existing Xcode install?
It could also have something to do with your include paths or something in that vein. I'm not too sure how to go about fixing that.
I would suggest backing up any custom templates etc. and running the uninstall script for both Xcode 3.x and 4, and then reinstalling to see if that fixes the issues.
Does this issue persist with XCode 3.2.5?
Just curious since I haven't downloaded it yet.