I recall reading about this before. If the server is empty all the soulshards work perfectly. If a player is only it despawns the mobs --- I thought the player also had to be in the same dimension to force them to despawn.
If mystcraft is available you might try putting your spawners in a world no one uses. If you just have the basic dimensions you might put them all in the end and have an agreement on the server to minimize time spent in the end.
I play on mindcrack so there is no mystcraft. But I do personally own the end. Tested and confirmed to work in SSP for my current modpack version. Thanks so much!