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Not sure if it will help with this particular problem, but if you haven't seen it already, there's some info here about how to work around a similar compatibility issues with FB4 and CFB sharing the same copy of eclipse:
I realize that the thread above is about installing CFB into Flash Builder, and that's the opposite from how you installed it. There are at least 4 different ways to install the two products:
I'm not clear on which combination works most reliably though (CFB into FB4, FB4 into CFB, or separate installs), but will ask around internally to see if we have some more explicit recommendations to offer.
Yes please do thx, its a pretty big important subject indeed.
I think my problem might be that I applied CF nature to my this flex project (to try and debug cfc's in the same project as a flex one) in the original standalone FB. How can I remove the CF nature, which should allow me to run this flex project.