I've posted this as a response to another thread, but since it was marked as resolved, I figure no-one at Jetbrains has read it...
The basic symptom is the project file is rewritten depending on the user in the team. Sometimes the change is a reordering of some elements. Other times dumb things like the debug port in a run configuration is changed - this one can happen for the same user (If the debug port is dynamic then the setting should say "dynamic" not change every time a new port is used). Or settings for a plugin are put there. This makes putting a project file under source control very difficult to manage without error because it's difficult to know if the change should really be committed.
Is there a way to prevent this? The closest I've come is to use the directory based format. Using this we can add the file names for settings files for individual developer plugins to the ignore list of the source control app, but we can't prevent the debug port from being overwritten or the elements from being reordered.
My Environment is Windows XP, JDK 1.6.0_10, and Idea 8.1 Build # 9732