I am having the same problem with Eclipse Juno, which I use for Android development.
As a workaround for Windows, I launch it from the console like this:
C:\path\to\eclipse\eclipse -clean
As hinted here, you can also try to delete the file YOUR_WORKSPACE/.metadata/.plugins/org.eclipse.core.resources/.snap
This also worked for me and (so far) seemed to fix the problem permanently, unlike the first option.