Hi lobster,
So you are having trouble updating just the virus definitions? If so, this might help -
Open the file /etc/freshclam.conf (as root) and look for a line, it is probably line 6 or so, that has "Example" in it. Comment out this line by placing a "#" in front of it (without the quotation marks). Save the file and see if it updates now.
I may be wrong, but do not try to update anything but the virus definitions. When there is a new GUI update, it is done through synaptic and not the program.
Hope this helps.