You're likely configuring the filters wrongly so that 'all folders' are not included. Make sure you use the *\ entry in your inclusion filters (as per the examples in the Help) as well as any file-based mask/s
Note also paragraphs 1-3 of my post here
viewtopic.php?f=16&t=10744&p=41653
and
viewtopic.php?f=29&t=9660
Note also paragraphs 1-3 of my post here
viewtopic.php?f=16&t=10744&p=41653
and
viewtopic.php?f=29&t=9660