Applied to FontExpert 8.0 Release 1 or earlier.
How to reproduce:
1. Open Find Fonts window, do not add any folder to "Search In:" list.
2. Clear the check box: [ ] Include Subfolders
3. Select the check box: [x] Search in Windows Fonts folder
Result:
2 copies of the same font file appear in the results list
(and incorrectly could be marked as duplicates).
How to workaround:
Select "[x] Include Subfolders" check box and repeat search.
This issue was fixed in the FontExpert 2006 version 8.0 Release 2.