I'm using NGG 1.2.1
After a file upload, if I use the "scan folder" function NGG deletes the new pictures of the folder/gallery.
I never had problems and it always worked.
Don't know what process deletes them but apache should not have the right to do it with this permissions:
Infact I also tried to remove every write permission to the files flags but they still disappear.
I also tried giving all permissions, of course, to the files.
Nothing to do.