I've had to fix this issue a couple of times (having forgotten how I did it the first time). Here's what you need to know:
AP doesn't know what to do with the M4VH brand which seems to be used by Quicktime when files are outputted for AppleTV, which didn't exist back when AP was originally written.
You can mod the code by following the directions in this post:
When I download the source (0.9) and open AtomicParsley.cpp, the lines are wrapped and line 1043 is no longer correct. You can find the correct place to insert this line:
case 0x4D345648 : //'M4VH'
by doing a search for this string:
metadata_style = ITUNES_STYLE;
The "Using AtomicParsley" text file included with the source include instructions for building the source. I ran into trouble doing this on Mac 10.6.3 and got this error:
i686-apple-darwin10-g++-4.2.1: obj_files/AP_NSImage.o: No such file or directory
Instructions for fixing this can be found here:
Build with these changes and you should be good to go.
This is helpful too for iphone:
case 0x4D345650 : //'M4VP'