Hi Dan,
important feedback for us. We have no opened customer issues that it would work only for one or two nodes. Would you mind to open a support case for this? Maybe it's something related to your environment only, but we would like to investigate and fix.
Regarding the ports that may see LLDP or Spanning Tree packets, you can utilize regex statement if there is a certain rule on your interfaces (name, description, etc.) that may identify this. If not, we would have to add special polling into this discovery process in order to provide you more visibility into interface "responsibility". The complete list would be very useful here.