I have. It generally means something was renamed or deleted in one branch and modified in another. (In your case, the repo and your working copy.) Subversion doesn't handle renames as well as I wish it did. :(
Essentially, this is a conflict -- but svn doesn't treat it like one, kind of. And I think it may behave differently in 1.6 (or maybe 1.5); what version are you using?
You'll have to go looking through the history a bit, along with your local modifications in your working copy and see what files and directories have moved around on either side. Once you've determined that, you can merge the bits and pieces together and move on.