I have been adjusting my moderator permissions and have some how lost the flag as spammer ability on mod accounts and admin accounts. I have the can flag members as spammer option on but the option is not showing on the forum. Is there another setting linked to its functionality?

Are you missing it for all members or just for some? Please keep in mind that administrators and moderators can't be flagged!

I would suggest to verify that the moderator permission is really set and if it is, submit a ticket, so that we can take a look at this for you:)

Thanks i submited a ticket. It was due to me addeding the member group as moderator with restricted permission. I had to add the group for a plugin (mark as sold) to work.

Got rid of that now and removed members group from moderators.