Handbrake 0.9.8 encoding unreadable files from MKVs off BD

[J.Lyman]

I am using MakeMKV to extract the main video title and it's corresponding audio track (DTS-HD, TrueHD, etc, whichever is the primary full channel audio track) and creating MKV files out of my Blu Ray discs I own. Afterwards I import them into Handbrake and encode them down to a more manageable size using the following:

bitrate: 12,500
audio: 1 passthru, 2 aac 6-channel discrete 640kbps
subs: none
container: mp4

The problem I'm running into is while I can test and confirm my settings to my liking by crunching say a 20 second clip from within the movie, encoding the whole movie results in a file that can't be read and tools like MediaInfo can't display any information about it. I did five movies that came out just fine this way, but when I started a second batch (and all subsequent batches), the files were useless.

Is there something I'm missing? What would you check first?

I apologize if this has been answered before. I didn't see a thread on this already and I wasn't sure if I was using the correct keywords to search.

Thanks in advance for your help.
-J

[vid.user]

Did you select the MP4 'large file size'?