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Issue moving site to ubuntu box - strange CI issues [solved]

I'm having serious difficulties moving my main site (codeigniter) to an ubuntu linux box.

The problems I'm having are not making any sense to me.

1. I have set my host and virtual host files to point to /var/www/mysite/v25_branch
2. I have set owner permission to me (user)
3. I can load in a virgin install of CI 2.0.2 with no problem - welcome screen displays.
4. I moved in my site - only to get a 404 on my main controller
5. The hang up is in Router::_set_default_controller() method, however; file is there and config.php and routes.php are set correctly.
6. I set logging to see what I could find out.
7. Log.php (system/libraries) cannot be found!
8. I stripped back to virgin install and started moving in files one by one.
9. Controller is found (my main controller) but error: Unable to load the requested file: navigation/navigation.php
10. As before, file is there. $this->load->view('header') was successful before this call, so load() works presumably.
11. Permissions are set recursively for all directories/files under path in point 1.

My live site runs on Linux - no problems there.
My dev site was typically on my windows box - never been any problems there.

I am putting this up in the hope that someone reading may pick up on something.

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