Hey, so I just ran into this, and I found that I could fix it by setting the value:
"LSRequiresIPhoneOS" to true (checked) in the application's Info.plist file.
I had a look back at all my old projects, and found that they all had this checked. I'm guessing that what happens is that when you open an old iPhone project in Xcode 3.2.3, it corrupts that parameter for some reason. I also encountered another other weird thing when I opened the project: a build parameter that is iPhone specific ("iPhone OS Deployment Target") was not there, and instead, the parameter "Mac OS Deployment Target" was there. This issue was resolved by saving the project. It all seems to point to Xcode failing to be backwards compatible with iPhone projects, which I've definitely seen other manifestations of in previous SDK upgrades.
Anyhow, hope this helps! If anybody has any deeper insights I'd love to hear them.