In following screenshot you'll notice changes that are so uncommited that they don't even care to show up!!!
I've seen even worse WTF's by the SVN plugin for Eclipse (SubClipse.)
On one installation of Eclipse, sometimes an update tries to merge two COMPLETELY DIFFERENT files. There's absolutely no connection between the two files, and their (differing) paths show up correctly in the merge window. Yet the plugin insists on merging the files, and more or less tries to replac the entire content, sometimes leaving an include or some parenthesis. It's ridiculous.
It's never happened on my own PC though, only in the lab where the project is located on a network drive, and a virus scanner is running. I can only imagine that that's the cause.