DigitalVolcano Software Support

Are there any limitations as to the number of subfolders in a search folder?
I am getting inconsistent results when scanning folders with a lot of subfolders. If i scan the subfolders individually, duplicates are found, if I select the parent folder, duplicates are not found. It is not too much of a hardship to scan several subfolders instead of the parent, but my concern is that there is no error or warning message, so I cannot trust the results.
I am using the pro version 4.10 and this behaviour has been observed with serveral versions before this.
I have just downloaded 4.12.....

No, there aren't any limits. Check you haven't set any other unwanted criteria and that 'scan subfolders' is set to 'Yes'. You can check your settings in the log file. If in doubt you can reset all settings in the Advanced options tab.

Also, it won't follow subfolders with a system flag (or a junction point).

Try unchecking:

-"Protect important system folders" - Options drop down menu
-"Don't follow NTFS Mountpoints and junctions" (Advanced search options)