If your Master Level Journal shows you have completed all the required encounters for a particular ML and your MLexp bar appears to be full yet the Arbiter will not grant you a new Master Level ability, you may be falling just short of actual 100% MLexp needed.
Here's what is happening: In order for the Arbiter to speak with you they must see you have completed X (100%) MLexp. You, after successfully slaying many Atlantis monsters (or enemy realm players) have tallied up X-1(or2) (99.99%) MLexp. The display differences between 99.99% and 100% are so small, it is hard to tell the difference. A few more monsters or enemy realm players will quickly solve the problem and allow the Arbiter to grant you that new Master Level ability.