No it didn't... it was always pure Light mobs, despite the Eidolon page throwing you into Fire Eidolons because of "mixed mobs." That got changed recently and it finally throws you into Dark Eidolons because the fight is against Light mobs.
The Light mobs each drop a guaranteed 650, 700 and 750 Gems. You get Gems accordingly to your kills. For the record, the Dark mobs drop you 40, 80 and 120 Gems.
I'm not saying that it's impossible that Dark mobs are spawning as holes, but I still find it unlikely.VeryVoodoo found a workaround for the empty waves.
1. Go join and kill a Raid battle
2. Close client
3. Log back-in and resume
Magically, the Light mobs will spawn back. It's a pain in the ass of a work-around, but at least you won't lose 25 AP. Just a boatload of time.