The major problem seems to be that once the experience bar reaches the level in which you can train the mastery rank, you are prompted to spend the mastery points repetitively despite weather or not you have the required mastery points.
three days prior to this comment I skipped ahead and did the beginning of the HoT story-line to unlock masteries. After they were unlocked, I begun to run around central Tyria and begin training Pact Commander. Before reaching the 4th rank, I saw the horror return. My exp bar started to blink again and the pop-up was back in full force.
I knew that I had to still unlock 3 mastery points to force the pop-up back into it’s cavern again. Thankfully; as far as Mastery points go, there was some low-hanging fruit so within 3-4 hours I had enough to rank it up and start training on the dreaded 5th rank of Pact Commander. I still need 6 more mastery points for it and I live in fear every day as my exp bar is already 1/3rd of the way there. and points are soon going to become more and more difficult to acquire.