hi 
that sounds familiar to me

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