With Ability Bar Timers active, casting a skill that grants a named buff (such as Major Sorcery) or applies a named debuff to an enemy will remove the timer for other skills that grant the same buff or debuff. For example, alternating Degeneration and Blue Betty will remove the timer for Blue Betty when you cast Degeneration, and vice-versa; casting Deep Fissure will remove the timer for Elemental Susceptibility.
This problem also extends to drinking potions; for example, consuming a potion that grants Major Sorcery will remove the timer for Critical Surge.
The skills remain active and continue to affect the player and enemies, this is purely a cosmetic issue with the displayed Ability Bar Timers.