Johannes,
Sorry that you are seeing problems with Webclipse. I have filed a bug report with the dev team for further investigation and we are also tracking the bug you filed in Eclipse Bugzilla. We will keep you posted when we have more information about the cause of the problem.
Can you please share with us the exact Eclipse version you are working with?
Apologies for inconvenience caused.
–Swapna
MyEclipse Support