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Since Eclipse 3.2M6, the option "Prompt for workspace on startup" in the "General/Startup and Shutdown" preferences doesn't seem to have any effect anymore. Eclipse always starts with the default workspace in the home directory, instead of prompting for the workspace to use. Switching the workspace still works.
Actually I'd classify this as major. It asks me the first time I launch after install but then never again. I find that deleting the org.eclipse.osgi folder in my configuration folder brings the chooser back.
*** This bug has been marked as a duplicate of 134412 ***