I really enjoyed this mode.

Well that is until new enemy cluster where created which had worms.

Checked the mod was active and the setting both checked,

Hi, thank you for using the mod.

Just re-tested and used the editor to generate huge amounts of chunks and the mod works normally.
Are you using other mods with it? try disabling all in a new game and leaving only this one to rule out.
This will only work for vanilla if you are using rampant it wont work.

normal spitters spawn win a new nest is made

Yeah, it looks like the initial generation of nests lack worms and spitters but future nests begin to have them.