There's a lot that goes beyond my knowledge, at least without referring to some books/the web. I'm curious as to why you have MyISAM showing under key buffer when you have InnoDB as your storage engine, but perhaps it's meant to be that way. InnoDB became the default with MySQL 5.5 and up but there are sometimes reasons to use MyISAM.
I was looking at the release notes for the version of MySQL you have and there are some bugs that might be somehow linked:http://dev.mysql.com/doc/relnotes/mysql/5.5/en/news-5-5-37.html
[Edit] Actually those seem to be bugs fixed from the previous version but the link for the next version might go into the bugs with 5.5.37.
Also, re: the part about joins:
Current join_buffer_size = 260.00 K
You have had 6845 queries where a join could not use an index properly
You should enable "log-queries-not-using-indexes"
Then look for non indexed joins in the slow query log.
If you are unable to optimize your queries you may want to increase your
join_buffer_size to accommodate larger joins in one pass."
That's a lot of joins that aren't using an index properly. MyISAM doesn't support foreign keys (if I'm not mistaken), so that could be interfering with joins if some tables are using MyISAM and others are InnoDB. However, it might not be an issue/problem/anything like that at all. It may be intended to be the way it is.