Having some really strange issues with my server/plugins

First off, I'll list my plugins for you, and they are all the latest build. http://d.pr/bhdy

1. ChatBukkit
2. CodeRedEconomy
3. Essentials
4. EssentialsHelp
5. EssentialsSpawn
6. EssentialsWarp
7. Guilds
8. iChat (config.yml)
9. ListPlugins
10. Permissions (config.yml)
11. Persistence
12. RealShop
13. ScrapBukkit
14. Spells
15. Wand
16. Whitelist

Now, based on this as reference, I'll give you the issues assosciated with each plugins

1. No apparent issues
2. No apparent issues
3. Mail does not work when send is attempted.
4. No apparent issues
5. No apparent issues
6. No apparent issues
7. Will not allow guilds to be created.
8. Will not show prefix/suffix
9. No apparent issues
10. Groups are ineffective, no users are given access to any commands, even the admins. See Permissions' Config.yml above.
11-16: All of these seem to be working correctly.

And here is the website for my server, in case you are interested in it. If you would like to connect to my server, give me your minecraft username and I'll whitelist you.

Any help is appreciated.

Edit: CraftBukkit version git-Bukkit-0.0.0-458-g5573d2-b440jnks (MC: 1.3)

Apparently is is also sporting some funky dev build of Bukkit.

And, on a side note, ladders are invisible when placed.