Yes, I tried everything but it seems to be a generic Eclipse error. My workaround today is a virtual machine (Virtualbox 14 GB ubuntu image) that boots ubuntu in Windows 7 and use ubuntu in the VirtualBox and then ubuntu can do it but of course I would prefer a native install.
I could not solve the java stacktrace and the only thing I could think was to upgrade the Java that Quartus uses to Java7 but would that make a difference using JVM 7 instead of 6? I think it might not make a difference since other users reported this problem as a generic Eclipse error using Eclipse with laptops that can't handle as many GUI widgets as desktop computer can in MS Windows. So I can use Ubuntu in a VM, use a desktop computer or upgrade Quartus to see if the issue persists in later versions.
Thanks for answering!