This evening I re-encountered a problem I came across a while back. It all happened when I was trying to get some comprehensively-named choons by Liberation Jumpsuit from my Gentoo box onto my Powerbook via Netatalk.
Despite having 10 tracks in the folder on the Gentoo box, the finder in OSX displayed the folder as empty. This is because AFP versions below 3 support a maximum filename length of 32 characters, and Netatalk 1.6.4 on my Gentoo box implements one of these older versions. The implementation in OSX has no such problems, so an OSX to OSX AFP connection should have no problems.
I gather from various postings on the web that there is a hack option to enable long filename support which breaks the protocol but works fine with OSX. I’ve yet to find it though.