Codeigniter site replicated in subdirectory not displaying individual pages - .htaccess

Question

We have just copied a Codeigniter website (from our root domain) to a subdirectory on the same root domain (with all config.php changes made and a new database etc.). However, page links don't display the individual pages yet the browser simply reloads the index.php page content (as if it's loading a new page) and changes the URL in the browser window to the correct page.
This is really odd and I've spent hours pouring over it, so I'm hoping someone here may be able to give me a starting search point.
For your information, the .htaccess in the subdirectory is:
RewriteEngine on
RewriteRule ^test.php$ mod_rewrite.php
RewriteCond $1 !^(index\.php|resources|robots\.txt)
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php/$1 [L,QSA]

Answer 1

if theres a new codeigniter install in a subdirectory now that used to be on the root, you need to include the name of the sub directory in front of the index.php parts of your htaccess
something like this(the change is on the last line):
RewriteEngine on
RewriteRule ^$ /dev/index.php [L]
RewriteCond $1 !^(index\.php|images|css|js|robots\.txt|favicon\.ico|zip\.php|resources)
RewriteRule ^(.*)$ /dev/index.php?/$1 [L]
dev should be changed to the name of your subdirectory. also, if neither or these works and you have a htaccess on your root, it could be effecting this subdirectory.

Answer 2

This is now sorted after a lot of different attempts!
File config.php in root -> application -> config (line 46) was originally:
$config['uri_protocol'] = ($_SERVER['SERVER_ADDR'] == '127.0.0.1') ? 'AUTO' : 'ORIG_PATH_INFO';
It should be:
$config['uri_protocol'] = ($_SERVER['SERVER_ADDR'] == '127.0.0.1') ? 'AUTO' : 'PATH_INFO';
All's now functioning correctly.