Hmm,

If this is happening, then there must have been some other changes to hook_order. I will look into this.

EDIT: It looks like hook_order was called twice for your setup wth $op 'update'. As we mentioned at the bottom of the included README, this could be an issue for certain setups. Also, as it says "We will be adding in a setting to only issue certificates on certain specified statuses.".

I hope everything is working for your setup now.