Are .MP3 files with capital letter extensions allowed in [audio] shortcode?

No, apparently not. Until this behavior is changed in version 3.7 you can add this filter to your theme’s functions.php file to include additional extensions.

Edited: I’ve updated the filter with better code suggested in the comments.

Lower case and uppercase extensions

function my_custom_audio_extensions( $exts ) {
    //merge array of upper case extensions with default array
    return array_merge( $exts, array_map('strtoupper', $exts) );
}
add_filter( 'wp_audio_extensions', 'my_custom_audio_extensions' );

Lower case, upper case, and first letter capitalized extensions

function my_custom_audio_extensions( $exts ) {
    //merge array of lower case defaults, uppercase and first letter capitalized
    return array_merge( $exts, array_map('strtoupper', $exts), array_map('ucfirst', $exts));
}
add_filter( 'wp_audio_extensions', 'my_custom_audio_extensions' );