I just had this issue, too, and found that it is because of the order by which the CSS and less are compiled. You need to use the style.less file. Copy that from the blank theme and I noticed that the .css files were then auto-generated with my custom CSS directory. However, any changes that would need to be made in the styles.less could most likely be made in the _theme.less. This is how I ultimately solved the issue. Within the _theme.less you can make specific CSS changes or make changes to variables like colors and such.
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