The files do not use identical formats, essentially:
Hubblecast: AVC1 profile High@L3.1 Constant fps
Auntie: AVC1 profile High@L3.2 Variable fps
High profile is 'broadcast standard' enoding profile, AppleTV doesn't officially support it only main profile - 3.2 and 3.1 may well differ apart from Constant/Variable fps, might be worth testing to see if 3.1 always works.
See:
http://en.wikipedia.org/wiki/H.264
AppleTv supports:
1 - H.264 and protected H.264 (from iTunes Store): Up to 5 Mbps, Progressive Main Profile (CAVLC) with AAC-LC audio up to 160 Kbps (maximum resolution: 1280 by 720 pixels at 24 fps, 960 by 540 pixels at 30 fps) in .m4v, .mp4, and .mov file formats
2 - iTunes Store purchased video: 320 by 240 pixels, 640 by 480 pixels, 720 by 480 pixels (anamorphic), or high-definition 720p
3 - MPEG-4: Up to 3 Mbps, Simple Profile with AAC-LC audio up to 160 Kbps (maximum resolution: 720 by 432 pixels at 30 fps) in .m4v, .mp4, and .mov file formats
...and some others if lucky.
In detail (download mediainfo:
http://mediainfo.sourceforge.net/en )
The clip that plays:
Complete name : working.mov.qt
Format : MPEG-4
Format profile : QuickTime
Codec ID : qt
File size : 6.83 MiB
Duration : 10s 0ms
Overall bit rate : 5 728 Kbps
Encoded date : UTC 1970-01-01 00:00:00
Tagged date : UTC 1970-01-01 00:00:00
Video ID : 1
Format : AVC
Format/Info : Advanced Video Codec
Format profile : High@L3.1
Format settings, CABAC : No
Format settings, ReFrames : 2 frames
Codec ID : avc1
Codec ID/Info :
Advanced Video Coding Duration : 10s 0ms
Bit rate mode : Variable
Bit rate : 5 724 Kbps
Width : 1 280 pixels
Height : 720 pixels
Display aspect ratio : 16/9
Frame rate mode : Constant
Frame rate : 25.000 fps
Resolution : 24 bits
Colorimetry : 4:2:0
Scan type : Progressive
Bits/(Pixel*Frame) : 0.248
Stream size : 6.82 MiB (100%)
Encoded date : UTC 1970-01-01 00:00:00
Tagged date : UTC 1970-01-01 00:00:00
The clip that doesn't:
Complete name : /notworking.mov.qt
Format : MPEG-4
Format profile : QuickTime
Codec ID : qt
File size : 5.32 MiB
Duration : 10s 0ms
Overall bit rate : 4 465 Kbps
Encoded date : UTC 1970-01-01 00:00:00
Tagged date : UTC 1970-01-01 00:00:00
Video ID : 1
Format : AVC
Format/Info : Advanced Video Codec
Format profile : High@L3.2
Format settings, CABAC : No
Format settings, ReFrames : 4 frames
Codec ID : avc1
Codec ID/Info : Advanced Video Coding
Duration : 10s 0ms
Bit rate mode : Variable
Bit rate : 4 461 Kbps
Width : 1 280 pixels
Height : 720 pixels
Display aspect ratio : 16/9
Frame rate mode : Constant
Frame rate : 25.000 fps
Standard : PAL
Resolution : 24 bits
Colorimetry : 4:2:0
Scan type :
Progressive Bits/(Pixel*Frame) : 0.194
Stream size : 5.32 MiB (100%)
Encoded date : UTC 1970-01-01 00:00:00
Tagged date : UTC 1970-01-01 00:00:00
AppleTv supports:
Video formats supported
* H.264 and protected H.264 (from iTunes Store): Up to 5 Mbps, Progressive Main Profile (CAVLC) with AAC-LC audio up to 160 Kbps (maximum resolution: 1280 by 720 pixels at 24 fps, 960 by 540 pixels at 30 fps) in .m4v, .mp4, and .mov file formats
* iTunes Store purchased video: 320 by 240 pixels, 640 by 480 pixels, 720 by 480 pixels (anamorphic), or high-definition 720p
* MPEG-4: Up to 3 Mbps, Simple Profile with AAC-LC audio up to 160 Kbps (maximum resolution: 720 by 432 pixels at 30 fps) in .m4v, .mp4, and .mov file formats
...and some others if lucky.