Ok, I did some extra testing. It's not all files. They are all MKV 1080p, but was not produced by same people. The one that doesn't work on PlexConnect do works on PLEX iOS client and PLEX web (it eliminates that the PMS can't work with those files).
Here is the MediaInfo of one of the files that doesn't resume (on those same files, there is also a issue when fast-forwarding and it tries to play when I hit play again it will 'spin' forever).
General
Unique ID : 222135854836299938565116289448454350882 (0xA71DCF38738904AF8A8FD42D73336822)
Complete name : File.mkv
Format : Matroska
Format version : Version 4 / Version 2
File size : 16.0 GiB
Duration : 2h 3mn
Overall bit rate mode : Variable
Overall bit rate : 18.6 Mbps
Movie name : World.War.Z.2013.Unrated.Cut.MULTi.1080p.BluRay.x264.AC3.DTS-HDMA-TMB
Encoded date : UTC 2013-09-03 10:03:31
Writing application : mkvmerge v6.3.0 ('You can't stop me!') built on Jun 28 2013 20:09:41
Writing library : libebml v1.3.0 + libmatroska v1.4.0
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 3mn
Nominal bit rate : 13.0 Mbps
Width : 1 920 pixels
Height : 800 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) : 0.353
Title : English
Writing library : x264 core 135 r2345 f0c1c53
Encoding settings : cabac=1 / ref=5 / deblock=1:-3:-3 / analyse=0x3:0x113 / me=umh / subme=11 / psy=1 / psy_rd=0.99:0.05 / mixed_ref=1 / me_range=64 / chroma_me=1 / trellis=2 / 8x8dct=1 / cqm=0 / deadzone=6,6 / fast_pskip=0 / chroma_qp_offset=-3 / threads=18 / lookahead_threads=2 / sliced_threads=0 / nr=0 / decimate=0 / interlaced=0 / bluray_compat=0 / constrained_intra=0 / bframes=5 / b_pyramid=2 / b_adapt=2 / b_bias=0 / direct=3 / weightb=1 / open_gop=1 / weightp=2 / keyint=250 / keyint_min=23 / scenecut=40 / intra_refresh=0 / rc_lookahead=250 / rc=2pass / mbtree=1 / bitrate=12990 / ratetol=1.0 / qcomp=0.60 / qpmin=0 / qpmax=69 / qpstep=4 / cplxblur=20.0 / qblur=0.5 / vbv_maxrate=50666 / vbv_bufsize=50666 / nal_hrd=none / ip_ratio=1.40 / aq=2:1.00
Language : English
Default : Yes
Forced : No
Color primaries : BT.709
Transfer characteristics : BT.709
Matrix coefficients : BT.709
Audio #1
ID : 2
Format : DTS
Format/Info : Digital Theater Systems
Format profile : MA / Core
Mode : 16
Format settings, Endianness : Big
Codec ID : A_DTS
Duration : 2h 3mn
Bit rate mode : Variable
Bit rate : Unknown / 1 509 Kbps
Channel(s) : 8 channels / 6 channels
Channel positions : Front: L C R, Side: L R, Back: L R, LFE / Front: L C R, Side: L R, LFE
Sampling rate : 48.0 KHz
Bit depth : 24 bits
Compression mode : Lossless / Lossy
Title : English
Language : English
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 : 2h 3mn
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 : 563 MiB (3%)
Title : French
Language : French
Default : No
Forced : No
Text #1
ID : 4
Format : UTF-8
Codec ID : S_TEXT/UTF8
Codec ID/Info : UTF-8 Plain Text
Title : French
Language : French
Default : Yes
Forced : No
Text #2
ID : 5
Format : UTF-8
Codec ID : S_TEXT/UTF8
Codec ID/Info : UTF-8 Plain Text
Title : Forced
Language : French
Default : No
Forced : No
Menu
00:00:00.000 : en:
00:05:05.179 : en:
00:13:53.999 : en:
00:22:43.195 : en:
00:29:46.034 : en:
00:35:21.494 : en:
00:42:23.457 : en:
00:52:37.946 : en:
00:58:53.821 : en:
01:07:18.868 : en:
01:15:11.757 : en:
01:24:02.037 : en:
01:29:08.801 : en:
01:34:50.518 : en:
01:43:45.469 : en:
01:52:17.981 : en:
01:55:51.653 : en:
02:03:03.417 : en:
Attached is also the PlexConnect.log with settings set to HIGH.
https://dl.dropboxusercontent.com/u/16957/PlexConnect.log