You might want to change the CSS you have added:
Here's what you have
Code:
#logoWrapper, {
#logo {float:left; width:490px; height:115px}  
#nihongoSiteButton {float:right; width:25px; height:115px} 
#animation {float:right; width:60px; height:115px} 
#line {background-image: url(http://english.globalpeace.jp/store/includes/templates/my_template01/images/logo/gpc-logo-trans-line.gif); background-repeat: repeat-x; margin:0 85px 0 490px; width:auto; height:115px}  
} /*Peace Freak - GPC Logo Added*/
You've included 3 IDs inside the LogoWrapper ID.
Make these changes and see if it helps
Code:
#logoWrapper, { }
#logo {float:left; width:490px; height:115px}  
#nihongoSiteButton {float:right; width:25px; height:115px} 
#animation {float:right; width:60px; height:115px} 
#line {background: url(../images/logo/gpc-logo-trans-line.gif) repeat-x; margin:0 85px 0 490px; width:auto; height:115px}  
 /*Peace Freak - GPC Logo Added*/