When using path auto relative links break.
If you have a block with an img that looks like:
Then visit some content that uses the alias content/node
the alias content is inserted into the img path, it comes up as content/sites/default/files/img.jpg which breaks the links.
Absolute links don't break or have the alias inserted. Only occurs when the actual domain is visited, not on temporary domains.
Not sure if clean urls affects it or not.