> Very probably a timer stops running just after system wake-up (after
> suspend to ram), because at that moment several timers are triggered
> at the same time.

I tried testing several timers going off at once, but reproduced no
problem.

;;; -*- lexical-binding:t -*-
(require 'cl-lib)
(let ((noninteractive nil))
  (cl-dotimes (timer-id 8)
    (run-at-time '(0 0 0 0)
                 0.1
                 (lambda ()
                   (message "%s DEBUG: Timer ID=%s" (current-time)
timer-id)
                   (sit-for 0 t)))))

All 8 fire without stopping.

Is it always the same timer that stops running, or have you seen
different timers in Emacs stop?

Could you come up with a recipe that allows us to reproduce the bug?