Hi,
When you change theme colors, do NOT touche the palette buttons afterwards, because palette simply copies a bunch of colors codes to ALL your theme settings so to make a dark/light... color scheme. it means if you have customized colors and then after that clicking a palette color scheme, you will lose all your previous color customizations. thats basically what palette is for,
But here is a good news
there is a new version uploaded in marketplace and waiting to be approved by IPS.
with the new version you can customize each of the color schemes in palette separately
you could even export your customized colors now