OS is Ubuntu Linux 15.10
the menu issue isn't a mouse or hard to use with mouse issue.
That specific edit metadata menu acts differently than all other menus all of a sudden (last few versions calibre) it flickers in and out as if you were running the mouse back and forth over it with the mouse just sitting still on it. also left click doesn't work to select option on submenu items. They highlight like they are selected but clicking doesn't do anything. once highlighted you can hit the enter key on keyboard and it will run that menu item. all other menu items other than that one work fine. You can use mouse to select and run them, no flickering etc..
on the conversion speed. I didn't know for fact that depending on what format to what format there was a difference in conversion speed, however it is logical. Mostly all I do is epub to mobi or azw3 as I use a kindle reader. I will have to start using azw3 as my default if that is that much faster. Over all it is not an issue. Nothing like the post of hours.
probably the worst I have seen is 4 or 5 minutes and normal is under a minute. Usually if I do a batch of 10 or so it might take 3 or 4 minutes. I had no idea some were having really long conversion times like described. I have never seen that even when doing from or to pdf which seems the longest to me. I just had noticed a difference of some taking 30 seconds to a minute at the fast end and 2 or 3 minutes on the long end
Wasn't a complaint at all just an observation that I didn't understand.