The first file is missing the Region_server.ini I beleive :( I will try to start that one up using the old file after I've grabbed some sleep. The settings editor is a nice touch, might make life easier for people wanting to run a server with this.
I was noticing, as I fire up my server, some of the map files don't seem to load successfully. Screenshots to be posted soon. Also, the documentation for the server files that were posted originally, makes no mention of running the update server at all, only the login, world, and region servers. The new server package adds the update server to the chain.
Without the update server I have been able to log in, run around town, but not actually get out to the game world proper to have a look around. Whether that's because I haven't explored enough or what I don't know.
@ Snaity, I assume your PHP script can be hosted on a system other than the one hosting the server? I'd rather try to get THAT part up and running on one of my linux boxes if possible, as I am running the server from a VM at the moment.