the rkhunter installation disables ssh protocol version 1 usage (which is good I would say) so you explicitely have to select protocol version 2 in your ssh client (putty?).
Maybe go into the server-manager remote access setting and change them to off, then back to on a minute later, for the ssh access part, so it will maybe reset any bad setting the upgrades had done.
I presume you regen'd the config file for ssh and informed SME of the change after the install completed:
Some time ago I also experienced this problem. It can be solved by removing the all openssh and SMEServer RPMs and reinstall them. Of course console access is required.