Hey Adam,
All these link colour is respected from this major colour from the template presets setting
http://take.ms/2u0A3 .
In order to show the immediately changes, ensure that you have to enable this setting
Compile LESS to CSS setting under advanced tab
http://take.ms/o5mmh .
And make sure that you have temporary disable your site cache if you have enable it from your site backend.
If you would like to change that hover link colour, unfortunately currently that is no setting for this, but you can try apply this following custom css into your template under custom css section
http://take.ms/mhCYe and see how it goes.
#vanilla-submenu > ul > li > span,
#vanilla-submenu > ul > li > a {
color: #eb4947 !important;
opacity: 1 !important;
}
#vanilla-submenu > ul > li > span:hover,
#vanilla-submenu > ul > li > a:hover {
color: #eb4947 !important;
}
Note : change this color code
#eb4947 to your current presets major link color code
http://take.ms/oxnmR
If it doesn't change anything, perhaps you can update your site backend and FTP access at
http://stackideas.com/dashboard/site so we can better have a check.