Have you upgraded your plugins to 1.5. If not, that could be the issue.
Checkout all your plugins in EPF 1.2.0.4, First upgrade to EPF 1.5, When
you start 1.5 with those plugins in your workspace, EPF should prompt you
to upgrade. Once upgrade successful, I think you will have to check in
those plugins again to subclipse. Let me know whether that does the trick.