I was playing, and no pixelmon were spawning. I checked the config, made sure all spawning was on, and still they were only spawning in the haunted tower and if you put down pixelmon grass.

Is this happening in a specific world, and if so, is it an extra overworld or something added by a mod, by any chance? This sounds like a dimension that's not configured to spawn anything. Logs may help.

I actually figured out the problem. I had a map installed that prevented things from spawning, but deleting the map did the trick. Thanks anyways.

Fair enough, closing!