I have the same problem: The initial GF installation was a v3 b57 on Ubuntu 9.04 / JDK 1.6.0_14-b08. I get the same exception after the last upgrade to 3.0.61 using the pkg tool.
I use NetBeans instead of Eclipse, but I have exactly the same problem: Starting GF from NetBeans succeeds more or less, with the above exception in the logs and sort-of active GF listening on ports 8080/4848, but the process cannot be controlled/stopped from NetBeans or the commandline, and has to be killed. Erasing the osgi-cache directory did not help.
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