I am having more issues and found a workaround! I had more stuttering issues with a downloaded tv show. Turns aut that switching deinterlace settings from auto to off fixes it completely. It is a 25FPS file on a pi2, I read some fixes are for Intel chipsets so not sure if this is related but it looks as if Kodi picks a deinterlace setting my pi2 can't handle (and playback is fine with it off, so it is not needed).
I don't understand how this works so will post all details and log, perhaps someone undertands what is going on
Full log uploaded to: http://ix.io/1ia6
-enabled debug log, rebooted, started playback (choppy), switched deinterlace to off (from auto), played a bit more (played fine
1. Playing with deinterlace on AUTO, it says it is using adv(x2) on my pi2. Playback is choppy and out of sync
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2. stats when playback is choppy. frame skips is stable at 2 strangely. buffer seems high
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3. choppy playback (deinterlace to auto) with debug log on (after reboot)
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4. With debug log still on same screen with deinterlace set to off
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Mediainfo on the file in question (downloaded, recorded tv episode)
General
ID : 1 (0x1)
Complete name : U:\Series\Cold Feet\Season 06\Cold_Feet_S06E08_NPO3_HD_VARA_20161216.m2ts
Format : BDAV
Format/Info : Blu-ray Video
File size : 2.97 GiB
Duration : 44 min 36 s
Overall bit rate mode : Variable
Overall bit rate : 9 526 kb/s
Video
ID : 4113 (0x1011)
Menu ID : 1 (0x1)
Format : AVC
Format/Info : Advanced Video Codec
Format profile : High@L4
Format settings, CABAC : Yes
Format settings, RefFrames : 4 frames
Format settings, GOP : M=3, N=15
Codec ID : 27
Duration : 44 min 36 s
Bit rate : 7 984 kb/s
Width : 1 920 pixels
Height : 1 080 pixels
Display aspect ratio : 16:9
Frame rate : 25.000 FPS
Standard : PAL
Color space : YUV
Chroma subsampling : 4:2:0
Bit depth : 8 bits
Scan type : MBAFF
Scan type, store method : Interleaved fields
Scan order : Top Field First
Bits/(Pixel*Frame) : 0.154
Stream size : 2.49 GiB (84%)
Color range : Limited
Color primaries : BT.709
Transfer characteristics : BT.709
Matrix coefficients : BT.709
Audio #1
ID : 4352 (0x1100)
Menu ID : 1 (0x1)
Format : MPEG Audio
Format version : Version 1
Format profile : Layer 2
Codec ID : 4
Duration : 44 min 36 s
Bit rate mode : Constant
Bit rate : 256 kb/s
Channel(s) : 2 channels
Sampling rate : 48.0 kHz
Compression mode : Lossy
Delay relative to video : 86 ms
Stream size : 81.7 MiB (3%)
Language : ned
Language, more info : Clean effects
Audio #2
ID : 4353 (0x1101)
Menu ID : 1 (0x1)
Format : AC-3
Format/Info : Audio Coding 3
Format settings, Endianness : Big
Codec ID : 129
Duration : 44 min 36 s
Bit rate mode : Constant
Bit rate : 448 kb/s
Channel(s) : 6 channels
Channel positions : Front: L C R, Side: L R, LFE
Sampling rate : 48.0 kHz
Frame rate : 31.250 FPS (1536 SPF)
Bit depth : 16 bits
Compression mode : Lossy
Delay relative to video : 31 ms
Stream size : 143 MiB (5%)
Language : ned
Language, more info : Clean effects
Service kind : Complete Main
Audio #3
ID : 4353 (0x1101)
Menu ID : 1 (0x1)
Format : AC-3
Format/Info : Audio Coding 3
Format settings, Endianness : Big
Codec ID : 129
Duration : 44 min 36 s
Bit rate mode : Constant
Bit rate : 448 kb/s
Channel(s) : 6 channels
Channel positions : Front: L C R, Side: L R, LFE
Sampling rate : 48.0 kHz
Frame rate : 31.250 FPS (1536 SPF)
Bit depth : 16 bits
Compression mode : Lossy
Delay relative to video : 63 ms
Stream size : 143 MiB (5%)
Language : ned
Language, more info : Clean effects
Service kind : Complete Main