Like Omni said, the only reason a new end world would generate is if a multi-world plugin is generating it. What plugins do you use,...
Also remove craftbukkit.jar from your plugins folder :P
I'd recommend using the official release of Sun Java 7 JRE for 64-bit. (dl)
I would recommend setting it to o (zero)
What exactly do you mean use it with bukkit? MySQL databases are used for plugins to store data, such as LogBlock.
Adminium is a iOS app that has /calladmin which is pretty useful if you have an iPhone with data.
What is the connection threshold in your bukkit.yml set to? What error does it say in console when you try to reconnect?
EssentialsChat uses c3p0, it causes problems with Factions and some other plugins if I remember correctly. I'd recommend removing EssentialsChat...
Try deleting the plugin folder and checking if it generates new files. If it does then the SQLite database is corrupted/malformed. Nonetheless, it...
As necrodoom stated, ModifyWorld plugin is blocking chat. You need to give the groups you want to allow chat the following permission.
Separate names with a comma.