A few of my ebuilds that have recently been marked as stable seem to be missing things from their manifests: !!! Security Violation: A file exists that is not in the manifest. !!! File: files/digest-gst-plugins-oss-0.6.4 gst-plugins-0.8.8 gave a similar error (except the file that wasn't in the manifest was digest-gst-plugins-0.6.4). Running ebuild [ebuildname] digest to regenerate the manifest clears it up.
Yuor sync mirror must have picked up portage tree in middle of my changes, the portage tre itself doesnt have same problems as your local copy. Please re-sync at appropriate time to ensure.