When something worked on Windows and started failing when it was moved to Linux, you're going to be looking at a few specific things, but likely won't need to change any code (with one exception):
- Capitalization of filenames must match the filename conventions required by the version of CodeIgniter you are using. With CI2 you're usually looking at all-lowercase filenames for controllers and models, while library class and filenames must use matching case (usually ucfirst). Check the documentation for any file type you're not sure about, or look at the code for the loader if you're comfortable reading through it for the filename handling.
- Permissions. Remember that, in most cases, the only thing that really matters for uploading is whether the account being used by your web server (usually www-data for Apache/Linux) has permission to write to the directory.
- Configuration differences between the server and the local environment (this is the exception in which you may have to change some code, but it will usually be in your /application/config/ directory or your .htaccess file). Of course, if everything else is working, most of the configuration is probably fine (unless you have an upload.php file in your config directory with some configuration error).
