[21:39:18 WARN]: java.lang.Exception: Apparent connection leak detected │
[21:39:18 WARN]: at me.confuser.banmanager.internal.ormlite.jdbc.DataSourceConnectionSource.getReadWriteConnection(DataSourceConnectionSource.java:120) │
[21:39:18 WARN]: at me.confuser.banmanager.internal.ormlite.jdbc.DataSourceConnectionSource.getReadOnlyConnection(DataSourceConnectionSource.java:102) │
[21:39:18 WARN]: at me.confuser.banmanager.internal.ormlite.stmt.StatementExecutor.buildIterator(StatementExecutor.java:243) │
[21:39:18 WARN]: at me.confuser.banmanager.internal.ormlite.stmt.StatementExecutor.buildIterator(StatementExecutor.java:217) │
[21:39:18 WARN]: at me.confuser.banmanager.internal.ormlite.dao.BaseDaoImpl.createIterator(BaseDaoImpl.java:954) │
[21:39:18 WARN]: at me.confuser.banmanager.internal.ormlite.dao.BaseDaoImpl.iterator(BaseDaoImpl.java:484) │
[21:39:18 WARN]: at me.confuser.banmanager.internal.ormlite.dao.BaseDaoImpl.iterator(BaseDaoImpl.java:475) │
[21:39:18 WARN]: at me.confuser.banmanager.storage.PlayerWarnStorage.findWarnings(PlayerWarnStorage.java:115) │
[21:39:18 WARN]: at me.confuser.banmanager.runnables.WarningSync.newWarnings(WarningSync.java:31) │
[21:39:18 WARN]: at me.confuser.banmanager.runnables.WarningSync.run(WarningSync.java:24) │
[21:39:18 WARN]: at me.confuser.banmanager.runnables.Runner.run(Runner.java:28) │
[21:39:18 WARN]: at org.bukkit.craftbukkit.v1_9_R1.scheduler.CraftTask.run(CraftTask.java:71) │
[21:39:18 WARN]: at org.bukkit.craftbukkit.v1_9_R1.scheduler.CraftAsyncTask.run(CraftAsyncTask.java:53) │
[21:39:18 WARN]: at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) │
[21:39:18 WARN]: at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) │
[21:39:18 WARN]: at java.lang.Thread.run(Thread.java:745) │

Getting that spammed though the config and what not is set up correctly.

This was already reported here and can be disabled in the newer dev builds:
#547
Dev Builds (check the changelog on Nr. 51)

Same issue as before. You can simply disable the leak detection.

However, by the looks of it, it seems like your syncing queries are taking longer than 3 seconds. Sounds like you may have a connectivity issue from your server to the database. I'd recommend running a ping from your minecraft server to the database server to check the latency and see if you receive any time outs to confirm.