Harry,
While the versions you typed in there look OK, this really looks like either an install issue or a corrupted workspace issue (although by erasing .metadata you are resetting it each time).
I would suggest a clean re-download of Eclipse 3.1.2 SDK and MyEclipse 4.1.1 from the respectives sites (even if you just downloaded them) and installation to clean *new* directories, don’t reuse old dirs and unzip ontop of old versions, this is a recipe for a mess.
Then try a new workspace, if that works, then try your old workspace. If that doesn’t work, try adding -clean to your command line options.