Content type node not overwriting the default node.tpl.php even if I have cleared all cache's I have a content type with a machine name of 'empresas' after reading the documentation I should be able to just create a node--empresas.tpl.php to toy with the output of this in my theme.

it seems to be not overwriting it. I am trying to hack something together and I am using the twitter bootstrap Drupal theme.

I have seem a similiar problem into another post in this forum but it seems like taht is not may problem because he have solve it by clearen all the cache's but that was not my case.
Initially, i say like not to override the original theme folder,

Create a sub theme of the base theme, in your case create a sub-theme of twitter bootstrap.
Then make the necessary changes in the sub-theme.

Enable only the sub theme.

And about overriding node.tpl.php file,
your approach is correct node--empresas.tpl.php, should over-ride the display of this particular node content.

Cross check machine name, Enabled theme, path of the overriding tpl.php file.