Are you copying via samba? It might be a permissions issue (you can check /var/log/samba4/log.smbd for NT_STATUS_ACCESS_DENIED messages). Try copying using winscp and see if the problem goes away. You can speed up transfers via SCP/SFTP if you use a crap cipher like arcfour128.
On the other hand, operations with lots of small files can be a pain point for Samba. If you look at 'top' output you'll probably see that you have a single thread pegged at around 100%. There are some operations that samba performs synchronously and this can harm performance when dealing with tons of tiny files. For instance, see discussion here:
http://marc.info/?l=samba&m=146175662822813&w=2
There are some things you can do to improve performance with lots of small files. Jeremy Allison outlines one strategy here:
http://marc.info/?l=samba&m=139336252926228&w=2
If you want to try out JRA's advice, please do it in the following way:
1) via WebGUI create new dataset with "Case Sensitivity" set to "Insensitive"
2) via WebGUI add auxiliary parameter to samba share "case sensitive = true"
This will significantly improve samba performance with small files (but may not improve speeds for initial transfer). Don't do the above steps if Case Sensitivity is important for you.