I could not reproduce the problem, via this recipe on Fedora 26 x86-64:

   wget https://elpa.gnu.org/packages/hydra-0.14.0.tar
   tar xf hydra-0.14.0.tar
   cd hydra-0.14.0
   make clean
   make emacs="$HOME/src/gnu/emacs/emacs-tmp1/src/emacs -Q" run
   [cut and paste the code in:
http://lists.gnu.org/archive/html/emacs-devel/2017-10/msg00160.html
   ]
   [C-x C-e after both expressions in that code]
   C-c l

where emacs-tmp1 is just after the commit in question 
(3db388b0bf83d3138562f09ce25fab8ba89bcc81), built from a fresh git 
checkout. I do not see the "binding stack not balanced" message.

Can you try the same thing as the above, and if you see the problem then 
let us know what .elc files you get? The .elc files I got are in the 
attached tarball.

What platform are you using?