It looks like the problem is that the code that converts from standard to wysiwyg is set up not to parse custom bbcodes, so they stay bbcode tags even in wysiwyg mode. fetch_tag_list() doesn't return the custom bbcodes, and when code in class_wysiwygparser.php does the standard to wysiwyg conversion, when it loads the custom tags, it changes the callback to 'handle_wysiwyg_unparsable'.
In any case, I don't know what you can do abut it short of editing vb files because there doesn't seem to be hooks in the right places. But if you were to edit the files, you could add your tag to the list of unparsed tags in class_bbcode_alt:
PHP Code:
/**
* List of tags the WYSIWYG BB code parser should not parse.
*
* @var array
*/
var $unparsed_tags = array(