Hi and sorry for this delay! I had my summer vacation the past couple of weeks so, unfortunately, I wasn’t able to reply earlier.
All the styles (colors, etc.) when the SmartMenus script is used with the Bootstrap add-on depend entirely on Bootstrap. So I did a quick investigation and figured out you need to tweak the @nav-link-hover-bg variable to change this background color setting:
But note that this will also affect any regular Bootstrap navs that have dropdowns. The reason for this “issue” is mainly due to the fact that Bootstrap doesn’t support multilevel navbar dropdowns by default and they have just not tested/considered a case where they are actually used.