I have had this problem. The way we solved it was by also committing the projectName.xcodeproj file. Basically, the whole top level directory that contained the resource files and project files were committed. We use the subversion system in the organizer. I'm not sure whether you are or are not committing the project file; but if you aren't I suggest you commit that too.
Since we started doing that, we have stopped having conflicts over the project file.
There is one other thing (and this is if you are committing the .xcodeproj file); when you commit, there is an unchecked check box under the .xcodeproj package. Make sure you check that. That way, the project structure changes will be relayed to all the other developers as well. :)
Hope it helps.