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I think the problem you are experiencing is this one:
You probably have Subclipse 1.2.4 installed, which is the latest official release. But the new release based on Subversion 1.5 has been in development for over a year. It will be version 1.4.0 and probably released next week when Subversion 1.5 is released.
I suppose it's possible but having 8 other developers using Eclipse for Java development not having issues while the Flex developers sooner or later end up with the Refresh Workspace fun..
Thank you for your post. I am researching your suggestion.
The issue I pointed to (which is the only one I am aware of that causes this behavior) is caused by a very specific, and fairly rare, project configuration. Basically, you have a single master project checked out and it contains nested projects that have been loaded into your workspace from the same physical location. If that does not describe your situation, then it is not the problem you are having.
turning off autobuild (project --> build automaticaly) option will also help.