Vanilla showing /home/user/public_html/ and editing .htaccess to fix.
Spent a little bit of time figuring this out so I thought I'd post it here.
Vanilla was showing /home/user/public_html/ instead of just the domain. Wat.
If you're having this problem and are using vanilla's .htaccess file on a fresh install this will probably fix your problem.
In the .htaccess file, change:
#RewriteBase / to
RewriteBase / or
If you look at the file it tells you what to do. Cool
It also suggests since you made a change to edit the first line from