Problem with HandBrake encoding only a part of a file

[Frozen Fractals]

I am having issues where HandBrake (http://www.videohelp.com/tools/HandBrake) (v0.99 on Windows 8.1 64-bit) is only encoding a part of a file. What I mean is that, let's say...for example, I have a 2 hours 44 minutes 33 seconds movie (metadata shown below) that I want to encode using the settings listed below. However, instead of encoding the whole file (all frames) like I tell it to, it is only encoding about half of it (1 hour 7 minutes 44 seconds to be exact). (NOTE: This happened twice - this along with another movie - in the past 24 hours and I am using only one of the occurrences as an example.) Why is it doing this and how can I fix it?

HandBrake Results:
http://i.gyazo.com/60c36c43fdda9aee983fc31b7c355442.png

HandBrake Settings:
- All chapters
- Mkv output
- Strict anamorphic
- Automatic cropping
- Default detelecine, Default decomb, off deinterlace, off denoise, off deblock, unchecked grayscale
- H.264 codec
- Same as source FPS
- Variable framerate
- Very slow preset
- Film tune
- High profile
- 4.1 level
- 18 CRF
- No audio, no subtitles, no chapters

Original File Metadata:
General
Unique ID : 331177862422873921685895677283931576227 (0xF926894570EB2D33456512715354D7A3)
Complete name : E:\The Dark Knight Rises (1080p HD).mkv
Format : Matroska
Format version : Version 2
File size : 32.7 GiB
Duration : 2h 44mn
Overall bit rate mode : Variable
Overall bit rate : 28.4 Mbps
Movie name : The Dark Knight Rises
Encoded date : UTC 2014-05-11 19:19:38
Writing application : MakeMKV v1.8.10 linux(x64-release)
Writing library : libmakemkv v1.8.10 (1.3.0/1.4.1) x86_64-linux-gnu

Video
ID : 1
Format : AVC
Format/Info : Advanced Video Codec
Format profile : High@L4.1
Format settings, CABAC : Yes
Format settings, ReFrames : 2 frames
Format settings, GOP : M=1, N=10
Codec ID : V_MPEG4/ISO/AVC
Duration : 2h 44mn
Bit rate mode : Variable
Width : 1 920 pixels
Height : 1 080 pixels
Display aspect ratio : 16:9
Frame rate mode : Constant
Frame rate : 23.976 fps
Color space : YUV
Chroma subsampling : 4:2:0
Bit depth : 8 bits
Scan type : Progressive
Language : English
Default : No
Forced : No

Audio
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 44mn
Bit rate mode : Variable
Bit rate : Unknown / 1 509 Kbps
Channel(s) : 6 channels
Channel positions : Front: L C R, Side: L R, LFE
Sampling rate : 48.0 KHz
Bit depth : 24 bits
Compression mode : Lossless / Lossy
Title : Surround 5.1
Language : English
Default : Yes
Forced : No