"Folder is 100% full (996 from 1000 messages stored)" does not seem too accurate, obviously. The line of code that determines this percentage is in functions_privmsgs.php:

		'percent'		=> ($user->data['message_limit']) ? (($user->data['message_limit'] > 0) ? round(($folder['num_messages'] / $user->data['message_limit']) * 100) : 100) : 0,

The use of the round function might not be appropriate here. Perhaps using number_format instead with the second parameter (decimals) being a 1 or a 2?