It's limitation of jQueryMobile framework: there is one "active" theme only that is common for all themes. The only way to change that color is to override it with css rules in template's css/custom.css, e.g.
.ui-btn-active {
border: 1px solid #2373a5 /*{global-active-border}*/;
background: #5393c5 /*{global-active-background-color}*/;
text-shadow: 0 /*{global-active-shadow-x}*/ 1px /*{global-active-shadow-y}*/ 0 /*{global-active-shadow-radius}*/ #3373a5 /*{global-active-shadow-color}*/;
background-image: -webkit-gradient(linear, left top, left bottom, from( #5393c5 /*{global-active-background-start}*/), to( #6facd5 /*{global-active-background-end}*/)); /* Saf4+, Chrome */
background-image: -webkit-linear-gradient( #5393c5 /*{global-active-background-start}*/, #6facd5 /*{global-active-background-end}*/); /* Chrome 10+, Saf5.1+ */
background-image: -moz-linear-gradient( #5393c5 /*{global-active-background-start}*/, #6facd5 /*{global-active-background-end}*/); /* FF3.6 */
background-image: -ms-linear-gradient( #5393c5 /*{global-active-background-start}*/, #6facd5 /*{global-active-background-end}*/); /* IE10 */
background-image: -o-linear-gradient( #5393c5 /*{global-active-background-start}*/, #6facd5 /*{global-active-background-end}*/); /* Opera 11.10+ */
background-image: linear-gradient( #5393c5 /*{global-active-background-start}*/, #6facd5 /*{global-active-background-end}*/);
}