Handbrake: Sound pops/blanks after conversion (likely DTS problem?)

I'm trying to track down a sound problem.

I'm finding in some recent Handbrake rips, some ...pops? hard to describe..every couple of moments there's a drop or a blank or a glitch (best I can think of) in the audio.

(described as blanks by 2 friends I sent the below sample to)

I found this checking the encodes on Beamer -> Apple TV -> Sony Receiver -> TV. I checked the file with VLC on the iMac, and they're there, so it's none of the set up beyond the file. I checked the original file I converted with Handbrake, so it's somewhere between Handbrake's conversion and the mac playback.

I'm using the Apple TV 3 preset.

I've seen it in several different files.
At least the sample file below has been played on 2 different macs and a Windows 7 desktop.

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There's 2 pops in this audio clip. It's the 20th Century Fox fanfare, so you should hear them easily at about the 9-10 second mark and the 16-17 second mark.
https://www.dropbox.com/s/d2tyktbd0ohfgv8/sound.m4a
or
https://dl.dropbox.com/s/d2tyktbd0ohfgv8/sound.m4a?dl=0

(I used Quicktime to trim the big file, then exported to audio only to make the clip)
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these are the settings...


(Subler used for the top 2 pictures)

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Can anyone suggest what's going on? This seems to be a new issue I'm running into.

(Handbrake Version 0.9.9 x86_64 (2013051800))

Ok, this file done in the same batch as the sampled one above doesn't seem to have the pop/blank problem..


The clear difference being the sound track of the original files, which despite playing with no issues in VLC, are converted differently by Handbrake.

I've tried the beta and nightly builds and different pre-sets with no luck.

Well no answers forthcoming at the handbrake forum..or here it looks like.