I'm having the same issue with it not getting the $WEB_ROOT/$BASE_PATH_JS and the correct URL is set in the SystemURL field in the tblconfiguration table. In my case WHMCS is installed in a sub-folder, not in a sub-domain so the affect is all the include paths are wrong. An example being
<link href="/assets/css/bootstrap.min.css" rel="stylesheet">
<link href="/assets/css/font-awesome.min.css" rel="stylesheet">
whereas in the head.tpl file it is
<link href="{$BASE_PATH_CSS}/bootstrap.min.css" rel="stylesheet">
<link href="{$BASE_PATH_CSS}/font-awesome.min.css" rel="stylesheet">
Since WHMCS is setup in the /clients folder it cannot find any of the include paths. I've tried using Aliases in the apache config to resolve this successfully however this breaks my website as it uses some of the same folder names.