Are you sure you added the right folder?
I just tried adding a hidden folder myself, and (at least for me) it didn't get included in the analyze...
Also, the code doesn't even 'see' if a folder is hidden or not... it just takes the location (i.e. 'C:\Whatever\Folder\Name\'), checks if it's in the ignore list, and doesn't scan it if it is...
My best guess is that you added the wrong folder... :/
(I really hope that's the case, cause else I don't know what the **** is going on

)