I kept receiving an errors related to filenames with capital letters for example system\core\Benchmark.php or system\core\CodeIgniter.php that they were missing. To solve it I had to extract the zip file from CI site in Windows and then copy it over. Doing this kept the exact file names without changing their names to lower case. Originally I extracted the zip file in ubuntu which automatically renamed Benchmark.php to benchmark.php which caused CI to have some major issues.
