I had exactly the same problem. The reason is when you uninstall via eclipse, it doesn’t delete the jar files from the plugin folder, the steps I did.
Go to folder eclipse/plugins for
avoiding any potential damage (just deleting wrong jars and get errors in other apps) list the jars from subclipse.
$ cd eclipse/plugins
$ ls |grep org.tigris.subversion
and then if it lists the following
$ ls |grep org.tigris.subversion
org.tigris.subversion.clientadapter_1.6.12.jar org.tigris.subversion.subclipse.doc_1.3.0.jar org.tigris.subversion.subclipse.tools.usage_1.0.1.jar
org.tigris.subversion.clientadapter.javahl_1.6.15.jar org.tigris.subversion.subclipse.graph_1.0.9.jar org.tigris.subversion.subclipse.ui_1.6.17.jar
org.tigris.subversion.subclipse.core_1.6.17.jar org.tigris.subversion.subclipse.mylyn_3.0.0.jar
Remove them by piping xargs rm to the command
$ ls |grep org.tigris.subversion|xargs rm
Restart your eclipse and you’ll only see the correct svn version.
PS: the .metadata you display comes from the workspace, it only affects to the projects you got from svn, it won’t do any change in eclipse.