Although generally speaking Sublime will load a
sublime-settings file from anywhere within any package, when it comes to the
User Package it seems to want to load them only from the top level of the package (i.e.
I believe this is due to the way that the settings system works in Sublime. Loading settings loads all of the files with that name from all available packages that contain the file, and saving the settings always puts them into the root of the
Hence, Sublime seems smart enough to not load settings from the
User package unless they're in the top level, as otherwise it would be impossible to edit settings that appear in the
User package without the non-root version contributing settings.
Generally how this would work would be that you would create an entirely new folder in
Packages for your syntax (e.g.
MVBasic); in there you would put your syntax file and the settings, and you can use whatever layout you want. A similarly named settings file (in the root) of the
User folder is for your user specific customizations to the default settings.
As a side note, the name of the settings file should mirror the name of the syntax, not the name of the scope that it applies; that may or may not be an issue, although you said that it worked until you moved the settings, so I'm just mentioning that for completeness.