Eadon,
The fact that you have to ask Eclipse to filter the files manuall, with an exclude, leads me to believe that you’re likely not using a Subversion client that’s an Eclipse plugin, but rather an external one instead. The reason that the distinction is important is that the Eclipse-based Subversion client properly marks the resources it uses as ‘team private’, which instructs both Eclipse and MyEclipse to ignore them automatically. You can get an Eclipse-based Subversion client here: http://subclipse.tigris.org/