I don't know if this is related but i experienced the same thing. Because of the glowstone bug MC-49126 we deleted the entire Nether (the DIM-1 folder). When it regenerated the terrain the spawners where missing.
Seed: 5422167314822212631 Coords for spawner: x:-396 y:76 z:-136
Jonas Albrektsson
I don't know if this is related but i experienced the same thing.
Because of the glowstone bug MC-49126 we deleted the entire Nether (the DIM-1 folder).
When it regenerated the terrain the spawners where missing.
Seed: 5422167314822212631
Coords for spawner: x:-396 y:76 z:-136