This post belongs in the Halp forums (individual character audit).
In what context? Do you have a log of 17k and another log in the same context of 13k?
Without understanding the context it's not possible to determine what you are doing wrong. It could be something trivial like you are comparing your starting DPS to your mid fight DPS in which case it's misunderstanding regarding how cooldowns work (front loaded damage). If its a particular encounter from week to the next it could be changes to the encounter (such as if you were comparing 4.0.3 Halfus to 4.0.6 Halfus, the boss no longer takes the additional damage immediately when a drake is released, you have to kill it before the damage increase is applied). It could also be variations in your group's composition such as losing the Sunder Armor / Faerie Fire debuff and forgeting to apply it yourself or losing a crit buff.