Jack:
I'm just another mineral owner; but, IMO all of that depends on the following. These are my thoughts.
#1. If the property/minerals under lease are in production, then unless you have something special written in your lease, then the minerals included in the pool will no longer be subject to a bonus until production has ceased and you get a release from the operator. From your post, it looks like you are getting production royalties.
#2. Any leased acres not in production should be subject to the bonus provision and most all operators pay that bonus before the first three year primary term expires. If the bonus is not paid prior to the first three year term, then my opinion would be that these acres are no longer under lease.
Good luck!