I have the same exact problem after following the moving wordpress tutorial my site works but it is style less i believe this has something to do with the permalinks, i already erased both .htaccess files from the root and from the install dir hoping wordpress would rewrite them. .htacess is created however the site is styleless while wordpress works seems to be working i believe this has to be with the modrewrite but i cant seem to find a explanation on how to fix it.
http://www.fernandoalvarezmusic.com
Moved the wordpress dir from http://www.fernandoalvarezmusic.com/blog to
http://www.fernandoalvarezmusic.com/system
current root .htaccess has the following.
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /fernandoalvarezmusic/system/
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress
