I randomly get this error on a onJoin or onQuit event:
http://pastebin.com/Up28mn3G
This is my config:
http://pastebin.com/w7NVAwsD
I'm using IPB.
I'm also using Spigot build 1434.
Have I configured things wrong or is this a bug?

You need some more configuration but it is also a bug that you get a stack trace instead of a notification of what is wrong.

PermissionsEx doesn't really have a notion of primary groups, so if you want to synchronize with IPB's primary group, you need to add the groups that are "primary" to the "groups-treated-as-primary" configuration option. Comma separated and in quotes is best: "guest", "member", ...

Ah! Sorry, I had no clue what these primary and secondary groups meant, so I pretty much ignored them. I will try this out though! Thank you 👍

Primary group: Most forums apps have the notion. Typically it is a group setting that a given player can only have one of (either a player is a guest or a member, not both).

Secondary groups on the other hand, a player could be a member of multiple secondary groups at time. Many forums have the concept.

Permissions systems tend toward not having a primary group idea; all groups are effectively secondary.