Have you tried one of the other themes? it might be the theme you using right now is the problem, in personalise/themes/theme settings there should be 3 default themes showing under the one you have selected. Any of these should let you swap the taskbar colours to black as it is the default colour, especially after you turn off Show colour on Start, taskbar & Action Centre
Also, the windows feature update is out and might fix this little bug you are having as it changes a lot of things to do with how win 10 works.