FFS not recognizing all sub folders

[MrToo]

I have recently accomplished a fresh build of Ubuntu Mate 24.04 on two different machines and installed FFS on both. The issue I have with both builds is that there are a few subdirectories/folders that are not recognized. However, I can browse to these unrecognized folders with FFS only to see the files with in these folders are now recognized. Now on an older PC with Ubuntu Mate 20.04 and same version of FFS I do not have the same experience and can recognize all files and folders. I have compared all FFS settings between PCs and can not find any difference. I am at a lost how to further troubleshoot this issue. I am sure I am missing something simple. Any suggestions?