A fix that worked for me, rather than renaming everything lower case, was to add an i modifier to the reg expression in plugin_basename() as below:
$file = preg_replace('#^' . preg_quote($plugin_dir, '#') . '/|^' . preg_quote($mu_plugin_dir, '#') . '/#i','',$file); // get relative path from plugins dir
This line can be found in wp-includes/plugin.php on line 572.
This worked with my install but I’m not sure what other implications it may have, so test before using!
