Installing wordpress on subdirectory 2 levels down

I managed to resolve this myself. Apologies for wasting anyones time. The fix was simple. I just had to add the following piece of code to my .htaccess 

<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /jack/blog/
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /jack/blog/index.php [L]
</IfModule>

Save my permalinks and the problem was solved. As I guessed it was a .htaccess issue and something I stupidly overlooked. Hope this helps anyone with the same issues as me.
Thanks

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