The only logical things I can think of is the original code that was copied contained the encoded equivalents of the code and the Custom Code text boxes were displaying the rendered equivalent code characters. We made some changes a couple of BPS versions ago to address that possibility so maybe that is why?
Or the other possibility is the .htaccess code was copied to and from an application like Microsoft Word. .htaccess code can only be copied to and from Notepad or Notepad++ otherwise the formatting of the .htaccess code will be corrupted and contain hidden formatting from Word, etc.