Do check Wheat's answer where he discovered the circumstances where OS X has a bug and the duplicates are caused by updating an App from the App Store.

For others where this isn't caused by a specific bug in Mountain Lion, the rebuilding has ruled out a stale launch services database, you should now rebuild your entire spotlight database.

This assumes you don't really have several copies of PDFPenPro - so you might run mdfind app_name before and after rebuilding spotlight since that is the likely cause of duplicate entries.

This might also be a good time to be sure your backups are current - random filesystem errors, incompatible utilities, or impending disk failure also could explain the database continuing to get rebuilt with duplicate entries.

Do check Wheat's answer where he discovered the circumstances where OS X has a bug and the duplicates are caused by updating an App from the App Store.

For others where this isn't caused by a specific bug in Mountain Lion, the rebuilding has ruled out a stale launch services database, you should now rebuild your entire spotlight database.

This assumes you don't really have several copies of PDFPenPro - so you might run mdfind app_name before and after rebuilding spotlight since that is the likely cause of duplicate entries.

This might also be a good time to be sure your backups are current - random filesystem errors, incompatible utilities, or impending disk failure also could explain the database continuing to get rebuilt with duplicate entries.

Since you have presumably ruled out a stale launch services database, you should now rebuild your entire spotlight database.

This assumes you don't really have several copies of PDFPenPro - so you might run mdfind app_name before and after rebuilding spotlight since that is the likely cause of duplicate entries.

This might also be a good time to be sure your backups are current - random filesystem errors, incompatible utilities, or impending disk failure also could explain the database continuing to get rebuilt with duplicate entries.

Do check Wheat's answer where he discovered the circumstances where OS X has a bug and the duplicates are caused by updating an App from the App Store.

For others where this isn't caused by a specific bug in Mountain Lion, the rebuilding has ruled out a stale launch services database, you should now rebuild your entire spotlight database.

This assumes you don't really have several copies of PDFPenPro - so you might run mdfind app_name before and after rebuilding spotlight since that is the likely cause of duplicate entries.

This might also be a good time to be sure your backups are current - random filesystem errors, incompatible utilities, or impending disk failure also could explain the database continuing to get rebuilt with duplicate entries.