Hi =)
I would like to point out that mineserver does not support everything the vanilla minecraft server does

1. Sound issue
Sounds were changed to be sent by the server at version 1.3 I believe, mineserver does not send any sounds at the moment
2. My map is blank and wont re-populate with info as I walk around.
Strange, it should generate the map as you walk around...
3. Pigs fly
All animals generated by mineserver are done by the plugins..which are not really useful yet =)
4. My inventory was askew
Yeah that might be a bug..but might also be fixed in the latest version...
5. My animal pens contents were gone. Gone! 30+ cows, pigs and chickens were replaced with ... 1 sheep and 1 chicken.
Mineserver does not use the animal information in the mapfiles..and there's not even a plugin that would handle the animal AI properly

6. The server says "no trees found spawning" when starting up every time it starts. My world has trees and mineserver doesnt appear to have generated any new ones or moved my old ones. A curiosity.
..right, thats just a debug message really. Mineserver saves all the saplings in the map and tries to load them.
Did I do something wrong? Remember I wasn't using any mods, maybe a few settings from within McMyadmin (things like view distance set to 6, allow snooping no etc) but I dont think those get stored in the map file anyways. Any help would be greatly appreciated. I really like the world that was generated and I'd like to keep it if possible. Thanks in advance.
No I dont think you did anything wrong, mineserver just handles things a bit differently. And you _should_ be able to use the maps already generated, we might have to fix something to make that work =/
Oh - one more thing. If there are some irreconcilable differences between server versions would it be possible for me to use the same world seed from my current server to generate the same terrain from within mineserver? and then maybe import player inventories/ a few chests for my and my pal? It would be a bitch rebuilding my house and re-exploring all the caves I have but if it must be done I guess I can. uhg 3 days of heavy play lost =/
The seed used in mineserver is completely different from minecraft, we have a custom generator so the map would be completely different even if you could input the seed =/
So basically you cannot do much about the problems, we would have to fix those in the code..
You could actually add those issues to our
bugtracker if you want to help out =)