Individual parts and or files of the following container types are not identified for viruses: PDF, ACE, BZIP2.
SMSMSE 6.0 has a limitation of not being able to open and extract files in the containers of PDF, ACE, BZIP2.
Upgrade to SMSMSE 6.5 or later.
SMSMSE 6.0 uses heuristic virus detection and may flag files of this type as infected. However, it is not able to open the file itself and mark individual files within the container as infected, meaning if it does find a virus, it will quarantine the entire file, not just the infected part.