Here is a mediainfo report on one of your encoded files. The one thing that strikes me as being a bit odd is the fact that the file appears to be reporting that the frame rate is variable between 24 to 30 fps.
I have a pretty good idea of what I would do to fix this though... download Handbrake (
http://handbrake.fr/downloads.php) and do a re-encode... I find Handbrake is great for most purposes. Try re-encoding it to a fixed frame rate 29.970 fps. I don't know enough to say if VFR will work or not..
Also, here is a technical document I found on Apple's website which seems to detail exactly what you are trying to accomplish.
http://developer.apple.com/iphone/library/technotes/tn2010/tn2224.html
Hope this info helps!!
General
Complete name : C:\YAMJ\Mediainfo\Test-40.m4v
Format : MPEG-4
Codec ID : M4V
File size : 15.3 MiB
Duration : 9mn 10s
Overall bit rate : 233 Kbps
Movie name : Test-40
Encoded date : UTC 2010-04-08 01:44:07
Tagged date : UTC 2010-04-08 01:47:07
Writing application : CoreMediaAuthoring 700, CoreMedia 484.5, i386
Video
ID : 2
Format : AVC
Format/Info : Advanced Video Codec
Format profile : Baseline@L3.0
Format settings, CABAC : No
Format settings, ReFrames : 1 frame
Codec ID : avc1
Codec ID/Info : Advanced Video Coding
Duration : 9mn 10s
Bit rate mode : Variable
Bit rate : 113 Kbps
Width : 640 pixels
Height : 480 pixels
Display aspect ratio : 4/3
Frame rate mode : Variable
Frame rate : 24.000 fps
Minimum frame rate : 24.000 fps
Maximum frame rate : 30.000 fps
Resolution : 24 bits
Colorimetry : 4:2:0
Scan type : Progressive
Bits/(Pixel*Frame) : 0.015
Stream size : 7.38 MiB (48%)
Title : Core Media Video
Encoded date : UTC 2010-04-08 01:44:07
Tagged date : UTC 2010-04-08 01:47:07
Audio
ID : 1
Format : AAC
Format/Info : Advanced Audio Codec
Format version : Version 4
Format profile : LC
Format settings, SBR : No
Codec ID : 40
Duration : 9mn 9s
Bit rate mode : Constant
Bit rate : 110 Kbps
Nominal bit rate : 128 Kbps
Channel(s) : 2 channels
Channel positions : L R
Sampling rate : 44.1 KHz
Resolution : 16 bits
Stream size : 7.20 MiB (47%)
Title : Core Media Audio
Encoded date : UTC 2010-04-08 01:44:07
Tagged date : UTC 2010-04-08 01:47:07