I have exactly the same problem with many MKVs of TV series.
When I show them with any media player on Windows or Linux or with OpenPLi without Autoresultion it's played correctly with 25fps.
As soon as I activate Autoresolution it's played back with 24fps and i have stutter every second.
I know it's an inconsistency within the media file, but why doesn't Autoresolution behave like any other media player?
Here is the MediaInfo output of an affected file:
General
Unique ID : 193831035115157693775464149124474485520 (0x91D27FDD22478EEB86D0C05382F83B10)
Complete name : /mnt/srvdata/MOVIES.HD/Monk HD/S07/Monk.S07E01.Mr.Monk.kauft.ein.Haus.DL.German.Dubbed.720p.WEB-DL.AC3.h264-FREAKS.mkv
Format : Matroska
Format version : Version 2
File size : 1.37 GiB
Duration : 41mn 24s
Overall bit rate : 4 749 Kbps
Encoded date : UTC 2010-04-03 18:45:46
Writing application : mkvmerge v2.9.7 ('Tenderness') built on Jul 1 2009 18:43:35
Writing library : libebml v0.7.7 + libmatroska v0.8.1
Video
ID : 1
Format : AVC
Format/Info : Advanced Video Codec
Format profile : High@L3.1
Format settings, CABAC : No
Format settings, ReFrames : 2 frames
Codec ID : V_MPEG4/ISO/AVC
Duration : 41mn 24s
Bit rate : 4 079 Kbps
Width : 1 280 pixels
Height : 720 pixels
Display aspect ratio : 16:9
Frame rate mode : Constant
Frame rate : 25.000 fps
Original frame rate : 23.976 fps
Color space : YUV
Chroma subsampling : 4:2:0
Bit depth : 8 bits
Scan type : Progressive
Bits/(Pixel*Frame) : 0.177
Stream size : 1.18 GiB (86%)
Language : German
Default : Yes
Forced : No
Color primaries : BT.709
Transfer characteristics : BT.709
Matrix coefficients : BT.709
Audio #1
ID : 2
Format : AC-3
Format/Info : Audio Coding 3
Mode extension : CM (complete main)
Format settings, Endianness : Big
Codec ID : A_AC3
Duration : 41mn 24s
Bit rate mode : Constant
Bit rate : 192 Kbps
Channel(s) : 2 channels
Channel positions : Front: L R
Sampling rate : 48.0 KHz
Bit depth : 16 bits
Compression mode : Lossy
Stream size : 56.9 MiB (4%)
Language : German
Default : Yes
Forced : No
Audio #2
ID : 3
Format : AC-3
Format/Info : Audio Coding 3
Mode extension : CM (complete main)
Format settings, Endianness : Big
Codec ID : A_AC3
Duration : 41mn 24s
Bit rate mode : Constant
Bit rate : 384 Kbps
Channel(s) : 6 channels
Channel positions : Front: L C R, Side: L R, LFE
Sampling rate : 48.0 KHz
Bit depth : 16 bits
Compression mode : Lossy
Stream size : 114 MiB (8%)
Language : English
Default : No
Forced : No
And here is the MediaInfo output of a correct file. As you can see the "Original frame rate" field is missing completely.
General
Unique ID : 234431999502370570920529747609338403551 (0xB05DF5F57181F7C8A0AB494F7CDA5ADF)
Complete name : /mnt/srvdata/MOVIES.HD/Monk HD/S06/Monk.S06E15.Mr.Monk.wird.gejagt.1.REPACK.German.DD20.Dubbed.DL.720p.iTunesHD.AVC-TVS.mkv
Format : Matroska
Format version : Version 2
File size : 1.49 GiB
Duration : 43mn 15s
Overall bit rate : 4 933 Kbps
Encoded date : UTC 2011-08-25 19:25:10
Writing application : mkvmerge v4.4.0 ('Die Wiederkehr') gebaut am Oct 31 2010 21:52:48
Writing library : libebml v1.0.0 + libmatroska v1.0.0
Video
ID : 1
Format : AVC
Format/Info : Advanced Video Codec
Format profile : High@L3.1
Format settings, CABAC : No
Format settings, ReFrames : 2 frames
Codec ID : V_MPEG4/ISO/AVC
Duration : 43mn 15s
Bit rate : 4 162 Kbps
Width : 1 280 pixels
Height : 720 pixels
Display aspect ratio : 16:9
Frame rate mode : Constant
Frame rate : 25.000 fps
Color space : YUV
Chroma subsampling : 4:2:0
Bit depth : 8 bits
Scan type : Progressive
Bits/(Pixel*Frame) : 0.181
Stream size : 1.26 GiB (84%)
Language : English
Default : Yes
Forced : No
Color primaries : BT.709
Transfer characteristics : BT.709
Matrix coefficients : BT.709
Audio #1
ID : 2
Format : AC-3
Format/Info : Audio Coding 3
Mode extension : CM (complete main)
Format settings, Endianness : Big
Codec ID : A_AC3
Duration : 43mn 15s
Bit rate mode : Constant
Bit rate : 224 Kbps
Channel(s) : 2 channels
Channel positions : Front: L R
Sampling rate : 48.0 KHz
Bit depth : 16 bits
Compression mode : Lossy
Stream size : 69.3 MiB (5%)
Title : monk-615-german-tvs
Language : German
Default : Yes
Forced : Yes
Audio #2
ID : 3
Format : AC-3
Format/Info : Audio Coding 3
Mode extension : CM (complete main)
Format settings, Endianness : Big
Codec ID : A_AC3
Duration : 43mn 15s
Bit rate mode : Constant
Bit rate : 448 Kbps
Channel(s) : 6 channels
Channel positions : Front: L C R, Side: L R, LFE
Sampling rate : 48.0 KHz
Bit depth : 16 bits
Compression mode : Lossy
Stream size : 139 MiB (9%)
Title : monk-615-english-tvs
Language : English
Default : No
Forced : No