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.
We probably mean the same, but it is the other way round. In WYSIWYG mode they do not stay as bb-codes, but you get the parsed result in your edit window.
I have done some more testing and in 4.1.3 it still worked as expected, this started with 4.1.4.