I've not come across this issue before. I have Subversion installed on my Linode and use WordPress's built-in automatic updates for security releases, everything works fine.
I use Subversion to add new WordPress installs because it's quick, but don't use it after that. Because of this I remove all the .svn folders immediately after installing WordPress - maybe this is your problem, the existence of .svn folders in the default WordPress folders?
If so, to remove them, cd to the root of your WordPress install and type this command:
Code:
find . -name .svn -print0 | xargs -0 rm -rf