Problem with HandBrake encoding only a part of a file

[Frozen Fractals]

I am having issues where 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:


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

[roma_turok]

Try with VidCoder
VidCoder is based on HandBrake

[Frozen Fractals]

Try with VidCoder
VidCoder is based on HandBrake

I will try that, but I am curious as to what is causing the issue at hand. Is it HandBrake, my setup, the files, or a combination of the above?

[roma_turok]

Did you use HandBrake 64bit version?

upload log file of encoding by going to Tools -> Option -> Advanced -> View Log Directory
in directory you can find logs of previous encodes, usual with name of video file

what happens when if you set preset to Normal without changing anything?

[Frozen Fractals]

Did you use HandBrake 64bit version?

upload log file of encoding by going to Tools -> Option -> Advanced -> View Log Directory
in directory you can find logs of previous encodes, usual with name of video file

what happens when if you set preset to Normal without changing anything?

Ok I think I have found out what is causing it. Whenever I am processing an encode and load the CPU with an additional task (i.e. a game, etc.) it "crashes". I have been able to repeat it thrice on demand. No solution to why it causes it to crash other than the presumption that it most likely "overloads" the CPU. Nevertheless, I'll just run my encodes overnight from now on as to not disturb the process.

[johns0]

Rip your disc again and re-encode.Might be a problem with the ripping.