I don't frequent these forums very often, so I just happened to come through here and see this post.
The physical machine you are on is backed up at 3:15 AM. Typical duration of the backup is less than 10 minutes.
We also backup the server's accounts separately so that we can restore cpanel specific information outside of the files in the public_html folder. That backup runs at 4:00 AM and typically takes about 30 minutes to handle all the accounts on the server.
It is possible that the slowness is related to one of those two activities as they both can be very I/O intensive. We have a fast RAID array on the server, but there is obviously a limit to what can be done these days.
If you have any other issues, please feel free to contact me using our office number, or the support system at https://billing.expresswebsystems.com/