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
2. stats when playback is choppy. frame skips is stable at 2 strangely. buffer seems high
3. choppy playback (deinterlace to auto) with debug log on (after reboot)
4. With debug log still on same screen with deinterlace set to off
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