If you download a changeset all files that contain ".svn" somewhere in its name are not downloaded. This is not limited to .svn directories, so also files named foo.svn.cs would not be downloaded.
repro: please try to download http://clonedetectivevs.codeplex.com/SourceControl/list/changesets
. The file /Setup/ConQAT/edu.tum.cs.conqat.svn.wxs is not contained in the zip file. Using Team Explorer, you can easily verify that the file exists. I assume you guys tried to exclude all .svn folders (presumingly because you are using the svnbridge to generate the zip files). However, as you can see: epic fail :-)