Styles for Nav-map macro are stripped out when displayed within the Documentation and Left Nav theme

Workaround available:
It seems like the navmap macro gets its styles from a CSS file called confluence.macros.advanced:navmap-resources.css For some reason, these styles are not getting applied to the nav-map macro output when displayed within the left nav theme. However, you can manually add those styles to each affected space using Confluence's stylesheets feature.

Pasting the contents of the confluence.macros.advanced:navmap-resources.css file (see below) into the stylesheets box should make your blue boxes come back. That should allow you to still use the nav-map macro with the left nav theme. The width and height parameters will allow you to specify the size of the nav-map boxes.

table.navMapContainer{background-color:#f0f0f0;margin:15px 0 15px 0;border:1px solid #ccc;}

table.navMapContainer th{color:black;font-weight:bold;font-size:14px;text-align:left;}

a.navMapCell,a.navMapCell:link,a.navMapCell:visited{background-color:#3c78b5;color:white;font-weight:bold;text-decoration:none;display:block;padding:10px;border:1px solid white;width:100px;height:25px;}

a.navMapCell:hover{background-color:#036;color:white;font-weight:bold;text-decoration:none;display:block;padding:10px;border:1px solid white;width:100px;height:25px;}