I faced a similar kind of situation. My development environment was WINDOWS and it worked fine as described in the DOCs i.e. MY_string_helper.php
On the production environment of UNIX, it gave error:
Unable to load the requested file: helpers/my_form_helper.php
Changing the file name to lower case resolved this error BUT the helper was not actually loaded.
After a lot of time waste, by hit and trail it worked [ it is un-documented ]
In the autoload.php, just include the mention the extended helper before the default helper:
$autoload['helper'] = array('my_string', 'string');
Also, the prefix has to capital, it did not work with lower case prefix:
$config['subclass_prefix'] = 'MY_';