Playing with this some more it seems to be related to using colors outside of the selected theme. If you stick to the theme colors, it publishes correctly, but if you select a color outside of the theme, it may be changed after publication.
Not good...I'm having the same issue. In this case, "0" are cases where something that should've happened has not happened, so I changed it to red, and switched the section that was defaulted red, and the rest of the colors remain the theme colors.
Power BI keeps changing the color that was originally red back to red when I reopen the saved file, which is...not good. It's happened on basically all of my charts in which I have done this, in different .pbix files.