Thanks for the debug. Things I saw wrong or potentially "out of place" you should consider fixing:
1. Upgrade the OS. You're on FreeNAS-9.3-STABLE-201412090314 , which is hella-old.
2. Some of your networking stuff looks fine, some of it seems "not quite right" which I could attribute to potential bugs in a FreeNAS build as old as yours. So I'd do #1 for two reasons. ;)
3. ada6 isn't 100% healthy. Not terrible, but it is likely starting to head downhill. It's failing SMART tests like crazy though, and has been for a while.
4. You should disable the hostname lookups for CIFS. It's not working on your network (nothing wrong with that, my network doesn't either).
5. Your log.smbd file has a crapload of errors and other very bad behavior. If you have SMB max protocol set to SMB3 I'd set it to SMB2. If you have any auxiliary parameters for CIFS/Samba set, I would remove them.
I get the impression that there's 3 possibilities:
1. You've done some reading and found some "tweaks" that are supposed to make things better on the FreeNAS, but they aren't helping (and most likely hurting).
2. Your desktops have some kind of "tweaks" that are supposed to make CIFS faster/better, but they're creating problems of their own.
3. You've got some kind of hardware issue that is not making itself immediately obvious.
Keep in mind that I can saturate 1Gb LAN (and do about 350MB/sec on 10Gb) using the default settings on FreeNAS as well as on my desktop. You shouldn't need to do tweaks and other things to saturate 1Gb. Your hardware was chosen pretty well, so I don't think this is an issue of you spec'ing out a system that is inadequate. I'd expect that your hardware should be able to saturate 2x1Gb LAN without breaking a sweat. Of course, that's not what you are actually seeing.
If you look at the debug file you sent me, and grab the file that is ixdiagnose\log\samba4\log.smbd you'll see all the errors I'm talking about. I've never seen them before, but here's a few:
[2016/03/23 00:15:25.856414, 0] ../source3/smbd/oplock.c:335(oplock_timeout_handler)
Oplock break failed for file Foto & Video/Canon EOS 600D/2013-04-04 Sälen, Lindvallen/IMG_3368.JPG -- replying anyway
As an option (if you are pretty sure you didn't do #1 or #2) then you could try this:
https://forums.freenas.org/index.php?threads/cifs-directory-browsing-slow-try-this.27751/ I wouldn't necessarily expect this to fix the issue, but it's worth a try since it's easy to implement.
Also you could try making sure you don't have things like "green mode" enabled on your desktop NICs, try disabling (or uninstalling) any firewalls and antivirus you have on your desktop, and make sure you aren't using Wifi on accident.