hook_block_view not being called
After looking around the code I ended up the _block_load_blocks function. Before calling drupal_alter('block_list', $block_info); I had 6 elements in $block_info. After the function had run I had 2 items.

Doing some digging in drupal_alter I fount out what modules were touching $block_info. The domain module was removing the blocks.

Looking at the settings on the block page I did not have my domain ticked. The message under the domain options did say:


  Limit block display to these affiliates. This block is visible on all
  domains by default using this theme.


So thought the block would appear by default. This was not the case.