Either backup configuration doesn't store or restore doesn't restore toolbar position and visibility (their contents are saved).
Have you set the toolbars as the default Toolbar Set, and made a new configuration backup since doing so?
I don't have a need for toolbar sets, so I haven't touched them.
In Settings/Toolbars/Toolbar sets menu, I only see something called Directory Opus 0.
You have a need for at least one toolbar set, since the default toolbar set is the toolbars you get by default.
A "Directory Opus 10" toolbar set will be created for your Opus 10 toolbars if you install Opus 11 over Opus 10. That lets you quickly reload your old toolbars if you don't want to use the new default ones. You still need to make them your default toolbar set if that's what you want them to be. (See the FAQ about this about 4 from the top of the FAQ list, from memory.)
Such an old answer, "Default toolbar set" - solved my problem first shot! Two minute search too ...