MKV audio and video stutter, fix or remux?

Ok, I've searched and read most of the posts relating to mkv's stuttering, however my tiny brain is not capable of understanding the issue
so please be gentle with me
I'm using the Panasonic 2010 profile on my TX-P50G20BA (latest version of Serviio and high spec PC, connected through homeplugs) and pretty much everything plays including most mkv's without any issues. An example I am having trouble with is detailed below (aspect ratio correct with black bars above and below):
Now, there is either something totally obvious in the above to everyone apart from me and there is a simple solution.....or I could remux (as I have done with PS3Muxer) into an mp4 where the stuttering disappears, however the aspect ratio gets screwed (stretched vertically) when I do this. The resulting mp4 is larger than the original, however, I have not noticed a reduction in the quality of the video (details of the mp4 below) and the bitrates are the same for both files.
Therefore my questions are as follows:
1. Is there anything in the above which I should beware of in mkv's?
2. If yes, can it be fixed to prevent stuttering? I assume by the posts I have read there is no clear solution and that remuxing might be the best way forward.
3. If remuxing, is there a way I can force the aspect ratio (in the Panasonic 2010 profile) to stay the same as in the original mkv when playing an mp4 (remuxed mkv with PS3Muxer) ?
4. If remuxing is the only answer, what is the best tool for it?
Much appreciated

I'm using the Panasonic 2010 profile on my TX-P50G20BA (latest version of Serviio and high spec PC, connected through homeplugs) and pretty much everything plays including most mkv's without any issues. An example I am having trouble with is detailed below (aspect ratio correct with black bars above and below):
- Code:
General
Unique ID : 176121867618419934911797495194306499691 (0x847FD67EB2EBD9E6B1BD8DE9A254546B)
Complete name : F:\Media\Film\Transformers Age of Extinction.mkv
Format : Matroska
Format version : Version 4 / Version 2
File size : 6.56 GiB
Duration : 2h 45mn
Overall bit rate : 5 684 Kbps
Encoded date : UTC 2014-09-18 20:51:00
Writing application : mkvmerge v7.1.0 ('Good Love') 64bit built on Jul 27 2014 13:06:55
Writing library : libebml v1.3.0 + libmatroska v1.4.1
DURATION : 02:35:41.832000000
NUMBER_OF_FRAMES : 2509
NUMBER_OF_BYTES : 80548
_STATISTICS_WRITING_APP : mkvmerge v7.1.0 ('Good Love') 64bit built on Jul 27 2014 13:06:55
_STATISTICS_WRITING_DATE_UTC : 2014-09-18 20:51:00
_STATISTICS_TAGS : BPS DURATION NUMBER_OF_FRAMES NUMBER_OF_BYTES
Video
ID : 1
Format : AVC
Format/Info : Advanced Video Codec
Format profile : High@L4.1
Format settings, CABAC : Yes
Format settings, ReFrames : 5 frames
Codec ID : V_MPEG4/ISO/AVC
Duration : 2h 45mn
Bit rate : 5 043 Kbps
Width : 1 280 pixels
Height : 536 pixels
Display aspect ratio : 2.40:1
Frame rate mode : Constant
Frame rate : 23.976 fps
Color space : YUV
Chroma subsampling : 4:2:0
Bit depth : 8 bits
Scan type : Progressive
Bits/(Pixel*Frame) : 0.307
Stream size : 5.69 GiB (87%)
Writing library : x264 core 142 r2479 dd79a61
Encoding settings : cabac=1 / ref=5 / deblock=1:0:0 / analyse=0x3:0x133 / me=umh / subme=7 / psy=1 / psy_rd=1.00:0.00 / mixed_ref=1 / me_range=16 / chroma_me=1 / trellis=1 / 8x8dct=1 / cqm=0 / deadzone=21,11 / fast_pskip=1 / chroma_qp_offset=-2 / threads=8 / lookahead_threads=1 / sliced_threads=0 / nr=0 / decimate=1 / interlaced=0 / bluray_compat=0 / constrained_intra=0 / bframes=3 / b_pyramid=2 / b_adapt=2 / b_bias=0 / direct=3 / weightb=1 / open_gop=0 / weightp=2 / keyint=250 / keyint_min=23 / scenecut=40 / intra_refresh=0 / rc_lookahead=50 / rc=2pass / mbtree=1 / bitrate=5043 / ratetol=1.0 / qcomp=0.60 / qpmin=0 / qpmax=69 / qpstep=4 / cplxblur=20.0 / qblur=0.5 / ip_ratio=1.40 / aq=1:1.00
Language : English
Default : Yes
Forced : No
DURATION : 02:45:07.273000000
NUMBER_OF_FRAMES : 237537
NUMBER_OF_BYTES : 6243731577
_STATISTICS_WRITING_APP : mkvmerge v7.1.0 ('Good Love') 64bit built on Jul 27 2014 13:06:55
_STATISTICS_WRITING_DATE_UTC : 2014-09-18 20:51:00
_STATISTICS_TAGS : BPS DURATION NUMBER_OF_FRAMES NUMBER_OF_BYTES
Audio
ID : 2
Format : AC-3
Format/Info : Audio Coding 3
Mode extension : CM (complete main)
Format settings, Endianness : Big
Codec ID : A_AC3
Duration : 2h 45mn
Bit rate mode : Constant
Bit rate : 640 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 : 756 MiB (11%)
Language : English
Default : Yes
Forced : No
Text #1
ID : 3
Format : UTF-8
Codec ID : S_TEXT/UTF8
Codec ID/Info : UTF-8 Plain Text
Title : English FORCED
Language : English
Default : Yes
Forced : Yes
Text #2
ID : 4
Format : UTF-8
Codec ID : S_TEXT/UTF8
Codec ID/Info : UTF-8 Plain Text
Title : English
Language : English
Default : No
Forced : No
Text #3
ID : 5
Format : UTF-8
Codec ID : S_TEXT/UTF8
Codec ID/Info : UTF-8 Plain Text
Title : English SDH
Language : English
Default : No
Forced : No
Menu
00:00:00.000 : en:00:00:00.000
00:06:51.578 : en:00:06:51.578
00:14:33.581 : en:00:14:33.581
00:21:37.463 : en:00:21:37.463
00:30:13.395 : en:00:30:13.395
00:38:45.990 : en:00:38:45.990
00:46:08.057 : en:00:46:08.057
00:51:39.513 : en:00:51:39.513
00:59:09.337 : en:00:59:09.337
01:07:48.648 : en:01:07:48.648
01:15:14.552 : en:01:15:14.552
01:23:25.292 : en:01:23:25.292
01:29:14.724 : en:01:29:14.724
01:37:16.956 : en:01:37:16.956
01:44:35.436 : en:01:44:35.436
01:51:25.053 : en:01:51:25.053
01:57:47.936 : en:01:57:47.936
02:04:48.481 : en:02:04:48.481
02:12:35.865 : en:02:12:35.865
02:21:04.206 : en:02:21:04.206
02:28:48.670 : en:02:28:48.670
02:37:09.629 : en:02:37:09.629
Now, there is either something totally obvious in the above to everyone apart from me and there is a simple solution.....or I could remux (as I have done with PS3Muxer) into an mp4 where the stuttering disappears, however the aspect ratio gets screwed (stretched vertically) when I do this. The resulting mp4 is larger than the original, however, I have not noticed a reduction in the quality of the video (details of the mp4 below) and the bitrates are the same for both files.
- Code:
General
ID : 1 (0x1)
Complete name : F:\Media\Film\Transformers Age of Extinction.mp4
Format : MPEG-TS
File size : 6.82 GiB
Duration : 2h 45mn
Overall bit rate mode : Variable
Overall bit rate : 5 913 Kbps
Maximum Overall bit rate : 35.5 Mbps
Video
ID : 4113 (0x1011)
Menu ID : 1 (0x1)
Format : AVC
Format/Info : Advanced Video Codec
Format profile : High@L4.1
Format settings, CABAC : Yes
Format settings, ReFrames : 5 frames
Codec ID : 27
Duration : 2h 45mn
Bit rate mode : Variable
Bit rate : 5 043 Kbps
Maximum bit rate : 40.0 Mbps
Width : 1 280 pixels
Height : 536 pixels
Display aspect ratio : 2.40:1
Frame rate : 23.976 fps
Color space : YUV
Chroma subsampling : 4:2:0
Bit depth : 8 bits
Scan type : Progressive
Bits/(Pixel*Frame) : 0.307
Stream size : 5.74 GiB (84%)
Writing library : x264 core 142 r2479 dd79a61
Encoding settings : cabac=1 / ref=5 / deblock=1:0:0 / analyse=0x3:0x133 / me=umh / subme=7 / psy=1 / psy_rd=1.00:0.00 / mixed_ref=1 / me_range=16 / chroma_me=1 / trellis=1 / 8x8dct=1 / cqm=0 / deadzone=21,11 / fast_pskip=1 / chroma_qp_offset=-2 / threads=8 / lookahead_threads=1 / sliced_threads=0 / nr=0 / decimate=1 / interlaced=0 / bluray_compat=0 / constrained_intra=0 / bframes=3 / b_pyramid=2 / b_adapt=2 / b_bias=0 / direct=3 / weightb=1 / open_gop=0 / weightp=2 / keyint=250 / keyint_min=23 / scenecut=40 / intra_refresh=0 / rc_lookahead=50 / rc=2pass / mbtree=1 / bitrate=5043 / ratetol=1.0 / qcomp=0.60 / qpmin=0 / qpmax=69 / qpstep=4 / cplxblur=20.0 / qblur=0.5 / ip_ratio=1.40 / aq=1:1.0
Audio
ID : 4352 (0x1100)
Menu ID : 1 (0x1)
Format : AC-3
Format/Info : Audio Coding 3
Mode extension : CM (complete main)
Format settings, Endianness : Big
Codec ID : 129
Duration : 2h 45mn
Bit rate mode : Constant
Bit rate : 640 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 : 756 MiB (11%)
Therefore my questions are as follows:
1. Is there anything in the above which I should beware of in mkv's?
2. If yes, can it be fixed to prevent stuttering? I assume by the posts I have read there is no clear solution and that remuxing might be the best way forward.
3. If remuxing, is there a way I can force the aspect ratio (in the Panasonic 2010 profile) to stay the same as in the original mkv when playing an mp4 (remuxed mkv with PS3Muxer) ?
4. If remuxing is the only answer, what is the best tool for it?
Much appreciated