Looks like iConomy is not saving correctly. The cause appears to be the use of persistent connections. Persistent connections are also causing problems with MySQL if the MySQL server times out (the JDBC doesn't handle the timeout correctly)
iDatabase.java has Connection.getConnection() but it never calls Connection.close() meaning it never releases the connection when its done.
[SEVERE] java.sql.SQLException: [SQLITE_BUSY] The database file is locked (database is locked)
[SEVERE] at org.sqlite.DB.newSQLException(DB.java:383)
[SEVERE] at org.sqlite.DB.newSQLException(DB.java:387)
[SEVERE] at org.sqlite.DB.execute(DB.java:339)
[SEVERE] at org.sqlite.DB.executeUpdate(DB.java:363)
[SEVERE] at org.sqlite.PrepStmt.executeUpdate(PrepStmt.java:85)
[SEVERE] at com.nijiko.coelho.iConomy.net.iDatabase.executeQuery(iDatabase.java:64)
[SEVERE] at com.nijiko.coelho.iConomy.system.Account.save(Account.java:94)
[SEVERE] at com.nijiko.coelho.iConomy.entity.iPlayerListener.showGrant(iPlayerListener.java:172)
[SEVERE] at com.nijiko.coelho.iConomy.entity.iPlayerListener.onPlayerCommand(iPlayerListener.java:522)
[SEVERE] at com.nijiko.coelho.iConomy.iConomy.onCommand(iConomy.java:133)
[SEVERE] at org.bukkit.command.PluginCommand.execute(PluginCommand.java:19)
[SEVERE] at org.bukkit.command.SimpleCommandMap.dispatch(SimpleCommandMap.java:77)
[SEVERE] at org.bukkit.craftbukkit.CraftServer.dispatchCommand(CraftServer.java:177)
[SEVERE] at net.minecraft.server.NetServerHandler.c(NetServerHandler.java:638)
[SEVERE] at net.minecraft.server.NetServerHandler.chat(NetServerHandler.java:601)
[SEVERE] at net.minecraft.server.NetServerHandler.a(NetServerHandler.java:595)
[SEVERE] at net.minecraft.server.Packet3Chat.a(SourceFile:24)
[SEVERE] at net.minecraft.server.NetworkManager.a(SourceFile:230)
[SEVERE] at net.minecraft.server.NetServerHandler.a(NetServerHandler.java:70)
[SEVERE] at net.minecraft.server.NetworkListenThread.a(SourceFile:100)
[SEVERE] at net.minecraft.server.MinecraftServer.h(MinecraftServer.java:351)
[SEVERE] at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:266)
[SEVERE] at net.minecraft.server.ThreadServerApplication.run(SourceFile:366)
[INFO] Player 50's account had 20.0 grant to it.
[INFO] ShadowDrakken tried command: stop
[INFO] CONSOLE: Stopping the server..
[INFO] Stopping server
[INFO] Goodbye world!
[SEVERE] java.sql.SQLException: cannot commit transaction - SQL statements in progress
[SEVERE] at org.sqlite.DB.throwex(DB.java:370)
[SEVERE] at org.sqlite.DB.ensureAutoCommit(DB.java:435)
[SEVERE] at org.sqlite.DB.execute(DB.java:332)
[SEVERE] at org.sqlite.DB.executeUpdate(DB.java:363)
[SEVERE] at org.sqlite.PrepStmt.executeUpdate(PrepStmt.java:85)
[SEVERE] at com.nijiko.coelho.iConomy.net.iDatabase.executeQuery(iDatabase.java:64)
[SEVERE] at com.nijiko.coelho.iConomy.system.Account.save(Account.java:94)
[SEVERE] at com.nijiko.coelho.iConomy.iConomy.onDisable(iConomy.java:119)
[SEVERE] at org.bukkit.plugin.java.JavaPlugin.setEnabled(JavaPlugin.java:142)
[SEVERE] at org.bukkit.plugin.java.JavaPluginLoader.disablePlugin(JavaPluginLoader.java:438)
[SEVERE] at org.bukkit.plugin.SimplePluginManager.disablePlugin(SimplePluginManager.java:199)
[SEVERE] at org.bukkit.plugin.SimplePluginManager.disablePlugins(SimplePluginManager.java:193)
[SEVERE] at org.bukkit.craftbukkit.CraftServer.disablePlugins(CraftServer.java:72)
[SEVERE] at net.minecraft.server.MinecraftServer.g(MinecraftServer.java:221)
[SEVERE] at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:296)
[SEVERE] at net.minecraft.server.ThreadServerApplication.run(SourceFile:366)
[INFO] [iConomy] Saved accounts and has been disabled.
Looks like iConomy is not saving correctly. The cause appears to be the use of persistent connections. Persistent connections are also causing problems with MySQL if the MySQL server times out (the JDBC doesn't handle the timeout correctly)
iDatabase.java has Connection.getConnection() but it never calls Connection.close() meaning it never releases the connection when its done.