If the audio track is disabled or the audio device discard all samples the bug doesn't reproduce
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vlc Game.of.ThronesS06E01.mkv
VLC media player 2.2.2 Weatherwax (revision 2.2.2-0-g6259d80)
[00007f1d9cc15f98] core input error: ES_OUT_SET_(GROUP_)PCR is called too late (pts_delay increased to 300 ms)
[00007f1d9cc15f98] core input error: ES_OUT_RESET_PCR called
[h264 @ 0x7f1d84c6a0b0] mmco: unref short failure
[00007f1d9cc15f98] core input error: ES_OUT_SET_(GROUP_)PCR is called too late (pts_delay increased to 545 ms)
[00007f1d9cc15f98] core input error: ES_OUT_RESET_PCR called
[h264 @ 0x7f1d84c6a0b0] mmco: unref short failure
gentoo-sources-4.5.3 has the same problem
My kernel configuration
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HD-Audio --->
(512) Pre-allocated buffer size for HD-audio driver
<M> HD Audio PCI
[*] Build hwdep interface for HD-audio driver
[ ] Allow dynamic codec reconfiguration
[ ] Support digital beep via input layer
[ ] Support initialization patch loading for HD-audio
<M> Build Realtek HD-audio codec support
<M> Build Analog Device HD-audio codec support
<M> Build IDT/Sigmatel HD-audio codec support
<M> Build VIA HD-audio codec support
<M> Build HDMI/DisplayPort HD-audio codec support
<M> Build Cirrus Logic codec support
<M> Build Conexant HD-audio codec support
<M> Build Creative CA0110-IBG codec support
<M> Build Creative CA0132 codec support
[ ] Support new DSP code for CA0132 codec
<M> Build C-Media HD-audio codec support
<M> Build Silicon Labs 3054 HD-modem codec support
-M- Enable generic HD-audio codec parser
(0) Default time-out for HD-audio power-save mode
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lspci
00:1b.0 Audio device: Intel Corporation 7 Series/C210 Series Chipset Family High Definition Audio Controller (rev 04)
01:00.0 VGA compatible controller: NVIDIA Corporation GK104 [GeForce GTX 760] (rev a1)
01:00.1 Audio device: NVIDIA Corporation GK104 HDMI Audio Controller (rev a1)
03:00.0 Ethernet controller: Qualcomm Atheros AR8161 Gigabit Ethernet (rev 10)
04:02.0 Multimedia controller: Philips Semiconductors SAA7131/SAA7133/SAA7135 Video Broadcast Decoder (rev d1)