are you using .emacs.desktop ? cause i use it and i have two situations at times yes i do use gnus wlust and mu4e
1) problems with monaco fonts overlapping as for bug 23360 temporarily solved by using xftfont.c from pretest 0.91 or a 2016-02-14 git clone i keep around
2) at times same 100 irresponsive cpu and swap loud grinding ;) in a word : box completely freezes i can only kill it from remote if i am already logged otherwise i can only hard reset yes : terrible bug
you are giving me some clues
that is something i am chasing from some time
to get my box alive i have to delete .emacs.desktop so i wonder if you can do the same and if we can blame xftfont.c or something else
in my case the freezes start if i ctrl right mouse popping the menu up options -> set default fonts to skip the the monaco fonts that as i said was overlapping