FSA not checking all subdirectories

Probably a simple config error on my part, but its got me stumped

I have set up FSA to archive an entire folder and it's subfolders. I have only one archive point and its at the top folder level and set for folders and subfolders.

When I either run an archive now or a report, it shows that it processes 1 volume and 1856 folders. The only issue is that I have 2421 folders in the volume.

I look through the report and see that many of my subfolders are not in the report and there are no shortcuts added in any of their files

Any idea where I could be going wrong here?

Thanks in advance,

Mark