S4 is called using the following instructions :

#!/bin/bash


cat /sys/power/state | grep disk
if [ $? -eq 0 ]; then
	date
	sleep 10
	# Clear old alarm
	echo '[CMD]echo 0 > /sys/class/rtc/rtc0/wakealarm'
	echo 0 > /sys/class/rtc/rtc0/wakealarm
        RC=$?
        if [ ${RC} -ne 0 ]; then
                check_rc "[CMD]echo 0 > /sys/class/rtc/rtc0/wakealarm" ${RC}
                return 1
        fi

	echo '[CMD]echo +40 > /sys/class/rtc/rtc0/wakealarm'
	echo +40 > /sys/class/rtc/rtc0/wakealarm
        RC=$?
        if [ ${RC} -ne 0 ]; then
                check_rc "[CMD]echo 40 > /sys/class/rtc/rtc0/wakealarm" ${RC}
                return 1
        fi

#	to change to /sys/class/rtc/rtcN/wakeup in future kernel
	dmesg -c >> dmesg
	echo '[CMD]echo disk > /sys/power/state	#S4'
	echo disk > /sys/power/state	#S4
	dmesg -c >> dmesg
else
	echo '[NOTE][CMD] S4 is not supported'
fi

echo "[CMD]suspend_resume end"

Does this still happen? If so could you try it with blacklisting the i915 and HDA drivers?

The problem is not present any more, i just run a short cycle (100 iterations), and it is coming back from S4 without problems.

Platform                        : BDW
Motherboard type                : NUC5i5MYBE Desktop
CPU family                      : Core i5
CPU information                 : Intel(R) Core(TM) i5-5300U CPU @ 2.30GHz
GPU Card                        : Intel Corporation Broadwell-U Integrated Graphics (rev 09) (prog-if 00 [VGA controller])
Memory ram                      : 16 GB
Maximum memory ram allowed      : 16 GB
CPU thread                      : 4
CPU core                        : 2
Socket                          : Socket BGA1168
Signature                       : Type 0, Family 6, Model 61, Stepping 4
Hard drive capacity             : 111GiB (120GB)


Kernel version                  : 4.9.0-rc5gcovjulian+
Linux distribution              : Ubuntu 16.04.1 LTS
Architecture                    : 64-bit
Mesa version                    : 11.2.0
xf86-video-intel version        : 2.99.917
Xorg-Xserver version            : 1.18.4
Intel GPU Tools version         : 1.14-1 <-- This is a generic version of IGT
Kernel driver in use            : i915