There are two known problems with SAM's internal backup functionality.
The first one appeared with MySQL 5.6 and is about write permissions for the MySQL server's Windows User.
A detailed explanation and solution can be found below.
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Another problem appeared with MySQL 5.7.6 (and newer) when a MySQL config setting changed it's default value.
That problem only appears when you install MySQL 5.7.6 or newer from scratch and doesn't affect existing installations where you simply update MySQL.
A detailed explanation and solution can be found in this thread: viewtopic.php?f=20&t=52387###
--- Original Thread content ---Resolving SAM backup errors with MySQL 5.6Multiple people have mentioned that when using MySQL 5.6, SAM backups and restores (using the Tools -> Backup -> Backup or Restore options from within SAM) are not working, and displaying an error message looking something like this:

This issue only happens when using the MySQL 5.6 installer, but not when doing a manual setup using the MySQL 5.6 zip file.
After some nice detective work by Jay and some others, we seem to have gotten to the bottom of the issue.
What seems to have happened is that the MySQL installer was changed, in 5.6, to set up the MySQL service to be run using the Network Service user account.
Previous versions (5.5 and earlier) set up the MySQL service to be run using the Local System user account.
The difference is that the Network Service account has very limited permissions to the local filesystem, especially to the user's application data folders and files, where the SAM application settings and backup folder is located.
The SAM backup system makes use of this MySQL service to create the database backups, so if the MySQL service doesn't have the correct permissions to access the backup folder, which is normally located within the users application data folder, at %localappdata%\SpacialAudio\SAMBC\backup, the backup won't be created correctly, and SAM will show the Backup failed message shown earlier, with the Permission denied message.
Fortunately, the fix for this is very simple.
The following guide should work on any version of Windows, but the actual screenshots were taken from a Windows 7 machine.
The simplest option seems to be to simply change the user that the MySQL service is running as, to now run using the Local System account, which will have the necessary access to the SAM backup folder.
In order to do this, we want to access the Services window. This can be done by clicking the Start button, and typing in services, and then clicking the Services icon that should show up at the top, with the gears icon:

You can also use the Windows key + R to open the Run window, and type in services.msc, or open Task Manager, click on the Serivces tab, and click on the Services... button in the bottom right corner.
Once that Services window is open, you want to locate the MySQL service in that list of services, which should be named MySQL by default.
Once you find that service, double click on it to open the service properties window.
Once it's open, click on the Log On tab on the top, and it should look like this:

As you should be able to see, the service is set to run using the Network Service account by default.
To switch it to use the Local System account, simply click on the "radio button" next to the Local System account option on the top, so that it now looks like this:

Once you do that, click on the Apply button on the bottom of that window, which should show you this message window:

This means that we will have to restart the MySQL service in order for it to start running using the newly selected Local System account user.
Click on the OK button on the message window, and and then on the OK button on the MySQL service properties window.
In order to restart the service, right click on the MySQL service in the Service window, and click on the Restart option.
A Service Control window should pop up, showing you while Windows stops and then starts the service.
Once that's finished, you should now be able to use the SAM backup and restore options without any issue:

An alternate fix would be to give the Network Service user permissions to access your %localappdata%\SpacialAudio\SAMBC\backup folder, but the above method seems to be the easiest and most reliable method.
As always, this is just a basic guide on how to make these changes to your system on your own, but please be cautious when making changes to Windows services, and make sure you understand what you are doing before you make any changes.