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When you first create the HTML, you can insert your tags, like < span > and then save it. It works nice. Then, if you edit the same HTML previously saved, it removes all 'personal' tags you added before load.
I have exact the same problem ...
The hidden textarea has all the formatin html tag but the editing iframe not
Only the span with the color class will be removed...
The "link" html tag (incl. target="_blank">) works O.o and any other formating like bold, italic and so on still works too.
I solved the problem.
I had an error in the color class names. In the bootstrap-wysihtml5.js the color class names were called e.g. "color-red" but the parser in the wysihtml5-0.3.0.js expected the class wysiwyg-color-red (see regex line 7025).
I rerenamed the color code names in the bootstrap-wysihtml5.js and all works fine.