iMac 21.5" Late 2009
Mountain Lion 10.8.5
Mail 6.6
I am having the same original problem. My "Not Junk" button is missing. It was there until recently, but now seems to have disappeared - after an update, no doubt.
I am not using the Cloud or any other Airy-Fairy software. Just bog standard Apple Mail.
I do not even have a Junk folder. My Junk setting is "Mark as junk but leave in my inbox". Just how I like it.
As I say, this used to work fine. A suspect mail would be coloured brown. I would click on it to expand it and on one of the top bars would be a button saying "Not Junk". If I wanted to keep the mail and similar mail in the future, I would click on that and the text would turn black. If it was junk I would delete it. Simple. Me in control of my computer.
Suddenly it's changed. The "Not Junk" button is not there. One solution from 2011 was to Ctrl-Click, the bar, select Customize and drag and drop the "Mark as Not Junk" (Thumbs Up) from the palette to the bar. 'Trouble is, there is no Thumbs Up button/icon in the palette.
I suspect an update, but I'm not sure, because the OS X update procedure was set to auto download and install. I've put a stop to that. It's now download and inform. I control my computer. I decide what goes on and when.
I've also had another oddity, with Safari 6.0.5. I used to be able to control the appearance of the Top Sites display. I don't mean the number of entries (Edit - Small, Medium Large), I mean what it looks like. I can't remember (and can't find) the actual description that I used; I think it was something like "Block". This produced equal size squares. Now it's gone to what I would call a depiction of a panoramic screen. Curving top and bottom, narrow in the middle and wide at the ends. There was another button in Top Sites Edit (might have been called View?) but it's not there now. Perhaps I should submit this as a Safari problem.
Also, when I clicked on Apple (symbol - top left) - About this Mac - More Info - OS X Support, I got sent to www.apple.com/nl/support. My Language setting is English, yet I was looking at a site in Dutch. I don't speak Dutch and would never have gone there voluntarily.
All of this has happened within the last few weeks. Any ideas/fixes? Have I been hacked? Or is an unknown auto update the culprit?
Thanks in advance.