Hi otropogo,
I'll restrict my comments to clamTK because that's the package I use. The latest version 5.03 is probably still in the "testing" stage and not classified as "stable" as yet. Eventually the latest version will show up in the Synaptic package manger. I too was tempted to update to the newest version and then thought better to be safe than sorry.
The important thing is that you update the virus definition files before running clamTK. You can do this by going to the "help" in the main menu and click on update.
As for your problem with the "software centre", I had a similar problem and it turned out to be a broken package. Try the following in a terminal to fix broken packages and dependencies:
Code:
sudo apt-get update
sudo apt-get -f install
Hope this fixes your problem.