Bukkit

Here's a few tips if you use Bungee with MaxBans:

Use Spigot... Please!

• Seriously. It's faster and designed for Bungee. Spigot is an active, faster, modded CraftBukkit by MD_5 over at http://www.spigotmc.org/.
• When you run your server, make sure in spigot.yml, under settings, the bungeecord-addresses list should contain your proxy IP (Eg, when players join through bungee, it will be wrong, and everyones IP will be the same. This IP that they all have should be in the bungeecord-addresses list!)

For CraftBukkit

• Recommend you use Spigot, but if you insist on CraftBukkit, in your config.yml you should set bungee: true in it if you use bungee. If you properly setup spigot with Bungee, then you should NOT use bungee: true.
• Using this setting is not recommended, but it is a workaround for IP's being incorrect. Players who are IP banned may still join temporarily, but will be kicked soon after.

Syncer

• Recommended you use this, guide is available here: http://dev.bukkit.org/bukkit-plugins/maxbans/pages/ban-syncing/
• Use the same MySQL database if you do this, whenever possible.
• Allows multiple servers to have the same banlist in real-time
• Allows banning users on ServerA while playing ServerB
• Revamped a fair bit in v2.0, so I recommend you grab that version instead of any previous ones!