Importing m4v files in AME fails....help?

Hi,
I have a problem that I have been unable to solve after months of trying.  I'm desperate for an answer or any help someone could provide.
I am using Mac Handbrake (Version 0.9.5 x86_64) to covert a few unprotected DVD's to .M4V (with video Codec: H.264).
I am then trying to bring these files into AME CS5 (Ver. 5.0.0.402 64-bit) to convert over to an .FLV or .F4V file for the web.  When I bring these files into the AME, no matter how long the videos are (typically 5-15 minutes long) it is showing the imported video as 3 seconds in length.  And when I go to render the .FLV file it renders, but only the 3 seconds.
Just for giggles I thought I would try the same thing in an older version of Adobe Flash CS3 Video Converter -- it had no problem importing the .M4V files and outputting the .FLV files at their full lengths.
Obviously, I would like to be able to use the new AME CS5, but have just been frustrated as all can be.
One additional point, when using Handbrake and using a different setting (Codec MPEG-4) the videos are recognized by AME CS5 at their full lengths, however the video quality is poorer.
Is there an issue with H.264 and AME CS5?
Any help would be greatly appreciated.
DMASH

What specific settings are you using in Handbrake?  (Screenshots of the settings dialogs would work well to communicate this.)
Can you post a sample of the H.264 output from AME that we could try?
AME should be able to import the H.264 file.  There could be a problem with the file Handbrake is creating, there could be a problem with your installation of AME, there could be a bug in AME, or it could be something else entirely.

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