WordPress multisite setup

Im trying to set W3 total cache on wordpress multisite to use amazon S3 but came across some problems.

I want the configurations to be global, i have ticked the “Use single network configuration file for all sites.” option. Everything works OK except that the urls that point to amazon s3(themes files) are adding the site folder aswell, which leads to a non existent file, example:

When i am on the main site everything works ok:
http://mysite.com/wp-content/themes/twentytwelve/style.css
changes to:
http://bucket.s3.amazonaws.com/wp-content/themes/twentytwelve/style.css.gzip?ver=3.6.1

When i am on other sites, example:
http://mysite.com/blog-name/wp-content/themes/twentytwelve/style.css
changes to:
http://bucket.s3.amazonaws.com/blog-name/wp-content/themes/twentytwelve/style.css.gzip?ver=3.6.1
it should be:
http://bucket.s3.amazonaws.com/wp-content/themes/twentytwelve/style.css.gzip?ver=3.6.1

I dont want to re-upload all the theme files for each of the sites, when all of them are using the same theme.

Any ideas on how this can be done?

Also getting an error message on subsites: Encountered issue with CDN: Table ‘event.wp_101_w3tc_cdn_queue’ doesn’t exist. See Install page for instructions of creating correct table. Although it seems to work.

Thanks

http://wordpress.org/plugins/w3-total-cache/