It appears that the default update parms have changed with the update I just did to Jenkins.
I updated Jenkins to 1.466.2 and all the plugins. The Jenkins CVS plugin is now at 2.7

At the start of the build, the CVS update used to look like this:
/Developer_4.2/usr/bin/cvs -q -z3 update -PdC -D "Friday, November 9, 2012 7:26:40 PM UTC"

It now looks like this:
cvs update -d -P -r HEAD -D 16 Nov 2012 01:56:11 -0600 workspace

So the builds are now failing any time there are any locally modified files. The -PdC used to take care of that.
-P Prune directories d create missing directories C Overwrite locally modified files

To the best of my knowledge, that isn't configured anywhere on our system and
the only updating done was the Jenkins updates. We do modify the .plists during the build, so it is expected
that they are locally modified. I can add a postbuild step to every build to delete the .plists, but that
isn't ideal. So it appears that something changed in the Jenkins CVS plugin to cause this to start happening or some other plugin that was updated.