I am trying to run some files encoded with license. When I load license file in .htaccess using:
php_value phpexpress.add_license "license.txt"
everything works ok.
But when I load licence in php.ini with:
phpexpress.add_license = license.txt
I get "no license loaded" error.
Phpinfo shows:

It seems that when loading license from php.ini only "Master Value" changes, but "Local Value" remains empty therefore this setting is not used and license is not loaded. I tested it on both Linux and Windows, php version 5.2.13. Is is a bug?

No, it is not a bug. Licenses loaded in php.ini work with stand-alone php or php-cgi.
In case of Apache modules, license loaded in php.ini are simply ignored, otherwise they would be valid for all the VHosts. That's why you have to add php settings in httpd conf -- the licenses loaded here will be valid for the VHost if they are loaded in appropriate part of the configuration.