Clash between WordPress site title and Seo Title of front page

WordPress version: 3.5.1
Wordpress Seo version: 1.4.4

I migrated from ‘All In One Seo Pack’ to ‘WordPress Seo’ recently and loving all its feature except I am having a little problem. I don’t know if I am the only one to face such a problem.

In the wordpress General Settings tab, you have the option to give your ‘Site Title’ and Tagline. If NO Seo plug ins are installed, then these information is seen in the search engines. But when I installed ‘WordPress Seo’ plug in, it had option to give ‘Focus Keyword’ ‘Seo Title’ and ‘Meta description’ in the seo optimization of front page/homepage. If I filled those with different data, then those would appear alongside with wordpress site title and tagline rather than replacing them. So, site title/homepage seo title and meta description/tagline began to appear in a repetitive manner (one from wordpress general settings and other from front page seo settings of the ‘wordpress seo’ plug in.) in google search engine.
Now, If I left those fields blank in the front page seo option, then the plug in would pick a seo title automatically and would appear together along with the site title in the search engine (google). The only solution that could resolve this problem is to keep the ‘site title’ and ‘tagline’ field blank in the ‘General Settings’ of wordpress. Then, only the data from the plug in (seo description of homepage) would appear in the search engine. But I am not sure if it is recommended to keep the ‘Site Title’ and ‘Tagline’ blank in the wordpress settings. I am worried this could affect my search engine ranking.
I hope you could suggest me a solution.

http://wordpress.org/extend/plugins/wordpress-seo/