Re-enabling them fixed the problem.

Resonant Rise.

Can confirm under Direwolf20 v1.1.1, running ender zoo 1.0.9.18. Very annoying as they seem to bypass walls and glitch out spawning containment setups.

Where the spawns disabled on both the client and server?
Needs to be done on both.
If this is not the issue I will need a crash log so I can investigate the problem.