I think I have the same problem, even after "apt-get -f install"ing.

One symptom is that after "Check for Updates" in the App Mgr, I get a buttload of entry pairs in the log like this:

apt-worker: Ignoring version from wrong domain: matchbox-window-manager 2:1.2-osso18
apt-worker: /var/lib/apt/lists/repository.maemo.org_dists_chinook_free_binary-armel_Packages

There are a few other log entries as well. Yes, I cleared the log before running this, and no, I don't know what these entries mean.

I can't really tell if it's degrading my IT performance but it doesn't seem right. (I was still able install the one update that came up and successfully installed "Othello" as a test.)