At some point all files in my working copy got marked with \"S\" symbol as shown below:
$ svn st
M S AclController.php
S InstallationController.php
There's another way in which this status can be achieved - which hopefully will save someone some time tracking it down.
I unpacked an external library into my SVN root, and it turns out the third-party author has accidentally included their own .svn folder in one of their folders. This of course overwrites our own, correct, subversion folder, and has the same effect as described elsewhere on this page - a folder appears to have switched unexpectedly to another branch.