1. Confirmed.
2. From what I can tell on your site, the search button is correctly using the vw_search_button style property. The color that's chosen in that property is correctly applying to the button. This is working as designed.
3. From what I can tell on your site, the filters drop-down in the recent activity block correctly uses the vw_control style property. The color that's chosen in that property (which by the way, uses XenForo's color palette and not a random color choice by us) is correctly applying to the button, and modifying the color does update the button. This is working as designed. If you have a custom style, you need to be careful about how you update your color palette to avoid clashes. In the case, of specific clashes, as in this case, you simply need to update the troublesome style property to give it a specific color rather than taking from the palette. Clashes often occur when users modify the -light(er)/-dark(er) palette swatches in such a way that the "light"/"dark" meanings are reversed or if "er"/"est" does not actually compare in the way the suffix implies.