That particular message should only be displayed when the book has no MOBI format (MOBI, AZW, AZW3, AZW4, or PRC), or the plugin can't properly parse the MOBI header info.
One or two really old (or badly malformed) MOBIs... I can see that happening, but if it gives you that message for every single MOBI you've ever tried it on, then something else is going on. How many are we talking about? Are they really mobi's, or do they just have the .mobi extension?