My first backup took awhile because it was 10+gigs of data. Of course it is going to take a while, you just upgraded your system and a lot of files changed. =)
Yup, I'm following the netatalk development closely. Apple has *finally* documented [1] what it takes to make an AFP server support timemachine backups and those changes are being coded up in netatalk.
Those warnings are just that, warnings. They don't prevent your backup from succeeding. I'm not worried about it right now because as far as I can tell, the default behavior is that if those commands aren't sent, then to assume the data is invalid and start over again. These new features will be added to netatalk and when there is a new release, I'll upgrade backmyfruitup to use it.