Custom mode on (not sure if that was the cause)

Any time I did something that would "update" my achievement list, the popup for achievements I've already gotten would appear.

examples: starting a new run would make the "unlock 10 weapons" and "unlock 10 skills" achievements pop up
killing ANY enemy would cause the "kill 100 elites" achievement to pop up (this was the worst offender since I would basically have the achievement popup on screen 100% of the time)