If you use a LOT of light (lava recommended) it stops them from spawning. You have to light something like a 5x5 cube centered on the spawner to get it stopped.
I should take a look inside my oldest grider to see if skeletons will spawn. I wound up filling it with dirt as a 'permanent' solution.
Egg not sure if you saw, but this was the same problem I had. I think zexx saw it. We spent a good hour filling in my entire "mob room" with dirt, started removing block by block, and they would spawn once a block was removed. We ended up filling the entire room with water at one point to drawn them as they spawned.
This was AFTER i removed all my spawners. Not sure what caused it, some kinda bug.
NOw adays they dont spawn in the blank spots anymore... it got fixed after something.
Maybe if G1 reboots the server it may fix his mysterious error also. I think it was stuck in the servers memory or something someone said.