A more drastic way: delete the whole .metadata folder.
Later import projects from their place or checkout them from the svn(if you use some). the problem is that we don't really know, what metadata are broken, so the natural next step is to delete all of them.
Once you have gone through all the optimization tips, Eclipse should start within 10 seconds and run much smoother than before.
: most of those tips will speed up your Eclipse experience, not just the startup time.
Is there any way to turn this off or at least speed this "refreshing" up?
UPDATE: It turns out that the solution was quite easy to resolve by closing projects that where not in use.
In order for Tip 3 to work, you will need to add the -vm setting in (see next section) This is one of the most confusing areas of Eclipse optimizations.