Why aren't my images not showing in my virtual sites libraries after uploading them to each?

Hi,

I don't know if this is related to Post Indexer or another plugin. I have uploaded pictures to each of my two virtual site through their corresponding media library. However, they do not show up in the library (just a broken image icon) and in the posts.

I've looked at their path in the library and it seems wrong to me since it is showing the main site/files/2013/03/and fies names for each instead of showing under each blog.dir/files path.

I don't recall which plugin took away and "re-adjusted" the permalinks. In fact, the permalinks are not showing in any of the admin menus, so i cannot do anything about them. Anyway, each site is using a different theme.

Is it something off in the htaccess or what?

Thank you for your help.

Kind regards,

Barb