While not necessarily a bug, the way custom brush materials work are a little counter-intuitive to those used to Photoshop. In Photoshop, saving brush presets doesn’t typically lock color information. In Manga Studio, it does by default, presumably to make it easier for users to import colored textures and objects.

If you use a normal color layer for a brush material, it retains all the color information. If you make a black ink splotch and save it as a material, it will always be black.

To get a brush to tint properly, the brush material layer must be set to gray scale inside of the program. The Layer Property panel above the Layer panel contains the Expression Color option. If you change that to grey scale then save your brush material layer, it will be able to change color.