I had the same problem but it occured while importing the theme-unit-test-data.xml along with its attachments. I am using WP 3.8.1. It’s a WordPress issue so editing the php.ini has no effect. WP uses a hardcoded value (60 secs) for http_request_timeout of WP_Http in class-http.php.
To solve it, place this code in functions.php of your currently active theme:
add_filter( 'http_request_timeout', 'mytheme_bump_request_timeout', 100 );
function mytheme_bump_request_timeout(){
return 300; //Change this to your desired timeout value in ms
}