I've seen this problem a few times, people having trouble getting the permissions right for websites. Heres a quick fix that will sort you in most cases
For directories run
find /path/to/domain/public_html/ -type d -print0 | xargs -0 chmod 755
Files run this one
find /path/to/domain/public_html/ -type f | xargs chmod 644
Make sure you change the path to be the correct path, and remember that some applications require a little more work. If you get stuck just drop us an email into support.