the new rkhunter kept your old rkhunter.conf, and placed the newer conf file under the name of rkhunter.conf.rpmnew. This was done in case you made changes to your rkhunter.conf file.
I had made one change to mine, so I'm glad that it kept it. I had changed:
ALLOW_SSH_ROOT_USER=1
The old conf file doesnt have all the new options, so if you have made any changes, transfer them to rkhunter.conf.rpmnew, delete the old rkhunter.conf, and rename rkhunter.conf.rpmnew to rkhunter.conf to make rkhunter happy.
This is not a bug...