Backup Exec 12.5 is backing up Empty folders

There are some options from Job Setup, Selection, Include/Exclude, but nothing automatic that I can see

Thats normal. They don't really add much space to the backup. I wouldn't suggest trying to intervene with that, because one day someone is going to have the idea to save a new file in one of those folders...and backup complications will arise on them.  If the folder is empty and you dont plan on seeing files in there you can just delete them I suppose.

I'm also reading your question a different way here...so disregard this part if I misinterpreted.

You say its backing up folders but they are empty. Are they empty when you are looking at them live? or are you saying the backups of the folder show nothing inside it? If its the latter, it may also be that the file(s) within that folder have not changed. Incrementals will only pick up new data so its possible that many folders will be empty.

The folders are not empty on the file server, none of the files under them have changed since the last backup.  I would have presumed because of that the folders wouldn't get backed up either.  

Our backup is very slow and I'm trying to optimize it, the drives I'm backing up have a deep folder structure and mostly 'small' files.  Figuring backing up folders was taking time also.

That's the thing, our backups should be flying.

We have a HP MSL2024 Tape library attached using Fibre Channel.  One of the drives has this summary for the Incremental.

Backed up 4 files in 13248355 directories.
Processed 3,074,481,490 bytes in  4 hours,  5 minutes, and  58 seconds.
Throughput rate: 11.9 MB/min
Compression Type: Hardware

That backup rate is crazy slow .  When I backup exchange and my sql data it flys.

Loaded the drives, they had the HP drivers on it.  That helped somewhat but nothing too big.

Talked to users and found folders that shouldn't be backed up or archived so that helped.

Good to know that the empty folders are backed up no matter what to retain the structure.