When it gets to that % it's probably performing the last step ... which is to *copy* the backup.mbz file in that temp directory to the destination as set in config.
On your server where is that destination? Bottleneck might be there.
Also, one can see a time there: 16:34:50 ... what else was going on with your server at that time?
Do you have MySQLTuner.pl installed? Do install it and run with DB superuser creds.
It is possible to set a variable too high and thus one gets deminishing returns on performance. Buffer pool should be slightly higher than data size:
[OK] InnoDB buffer pool / data size: 4.0G/3.1G
InnoDB buffer pool / data size - if you increase buffer pool, one should also increase the number of instances according to recommendations made by Tuner.
Buffer Pool 4 G
should have Buffer Pool Instances of 4 as per example given.
The above values, BTW, from a live server that has fewer courses than yours and fewer users as well.
'SoS', Ken
by Ken Task.