René,
If this is on MyEclipse 7.0 the update sequence runs in the background to maintain the integrity of the workbench (and is part of a bigger feature set that will be rolled out shortly).
Are you behind a proxy by chance? If it’s setup incorrectly that update sequence can barf *but* when it barfs it should fail gracefully/quietly and it sounds like it’s not doing that.
Could you paste your information from MyEclipse > Installation Summary > Installation Details here for me?