I noticed this in a raid context that with the Dark Rites effect active on me, the act of changing spell sets (unmemorize, memorize) consumes charges from the spell effect. I verified this today in my guild's hall while not distracted by the goings on of an event.
Do you have any buffs/auras/songs that are ticking on you? There's stuff that will consume some kinds of counters when it ticks because it's counting as a spell cast.
At raid time, very likely but in the guild hall there was only the regen aura. It's possible this ticked, but it seems to be a continuous effect like a Twincast aura.
It's very easy to test and see. Has nothing to do with twincast or other buffs/songs/auras. I tried a dd spell, buff, and a create mana item add in an empty spell bar slot. Once added to the spell bar, the Rod buff counter ticked down on all 3 spell types. Casting a spell with a long recast did not make another counter disappear when it repopped. So it only seems to be newly added spells to the spell bar and the counter loss occurs when that new spell has finished adding.
To clarify what I said in reply to Soulbanshee, and confirm what Cragzop said: No active ticking effects (hall aura, bard songs, etc), if I unmemorize a spell and then memorize a new one, I lose a counter on the Dark Rites effect.
