After documenting problems that I had with AtomicParsley and HandBrake files was a frustrating experience.
It happened to me every time but did not happen to others all of the time.
What finally appears to be be the problem is easily avoided, if you don’t use the AppleTV preset.
Large File Size
All of my files were created with the AppleTV preset in HandBrake. Most of the shows that I will be watching will be either on my iMac (which can play AppleTV files) or my AppleTV, so it made sense.
However, the AppleTV preset in HandBrake 0.9.3 adds a new feature called “Large File Size”. What is “Large File Size”? This is what the command-line version of HandBrake (HandBrakeCLI) says:
-4, --large-file Use 64-bit mp4 files that can hold more than
4 GB. Note: Breaks iPod, PS3 compatibility.
There isn’t a whole lot of information about this option in the HandBrake documentation, but if you hover over the option in HandBrake you will see a tooltip:

The take-away point here is whenever you see “Large File Size” think “64-bit” not necessarily “4GB”.
The nomenclature here is confusing. If you use this option, you will not necessarily get a 4GB or large file (an average episode of the West Wing (about 42-44 minutes without commercials) is 400-650MB. However, these are still “64-bit” files, and that seems to cause the problem with AtomicParsley.
This option according to some discussion on the HandBrake support forums.
My recommendation is that you do not use this option unless you know that you need it (i.e. you are ripping a very long movie). I do not know what happens if you try to make an AppleTV compatible file of a movie and it needs to grow larger than 4GB, but it seems unlikely to be something that we run into often.
Make Your Own Preset
One of the nice things about the GUI version of HandBrake is how easy it is to customize a preset.
Step 1: Choose the AppleTV preset in HandBrake (click “Toggle Presets” if it isn’t visible already)

This will get you most of the way there.
Step 2: UNcheck the “Large File Size” box
- All three ought to be unchecked:

- Then go back to the Sidebar and click the +

- Give it a name, something clear and obvious:

- After saving, make it the default (if you wish)

Using those settings should help you avoid the AtomicParsley bug I have been struggling with.