Xcode not saving source files

Hi
Has anyone else come across an issue where Xcode doesn't save source files before a build - despite setting the For Unsaved Files preference correctly?
My Java students are using Xcode 3.1.1 to create and build Java Tool projects. We've noticed that we can't modify the default source file for a newly created project, nor can we modify any new source files we add to the project UNLESS we close down and restart Xcode after adding each new file. Specifically, any edits are stored in the file buffers but these are not automatically saved to the hard disc when we trigger a build. However, once Xcode is closed and restarted, all source files in the project behave normally.
Interestingly, the problem doesn't seem to happen with Tool type projects in other languages, however, these projects by default put the source files in the top level of the project folder, whereas all Java projects put the source files one level down in a "src" sub-folder.
Has anyone else noticed these issues with Java projects? Do similar problems occur in other languages if source files are stored in sub-folders? Remember, the problem only exists for newly created files and it's resolved once Xcode is shut down and restarted - unless, of course, we need to add more files.
Anyone got any workarounds which avoid stopping and restarting Xcode?
Bob
PS: Please don't post comments saying that I should use Eclipse, Netbeans, BlueJ, etc That's not relevant to this discussion.

Thanks briyu. At least you've confirmed that I'm not going mad
As for 3.1.0, that's what the student machines are using and we have the problem there. I wonder why no one else has reported this before? Probably Xcode isn't used very much for Java.
Bob

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