Media Encoder not keeping duration metadata

Ok, first off, I'm still new to using the Media Encoder, so I am asking, if you have a solution, please feel free to treat me like a 3-year old or like someone who doesn't know how to change their own tire.  Yes, I am asking of hand holding here, mainly because I've scowered too many forums and done too many searchs through Google to come up empty handed.
So here's the situation:
My company is doing our own videos for our products, as well as created our own media player that has the ability to play one video after another.  The videos are created in Final Cut and are given to me as .mov files.  I then put them into the encoder and turn them into .flv files, using the preset FLV - Web - 768X432, 16X9, Project Framerate 900kbps.  Through my searching I found that the Media Encoder should automatically bring in the duration, but maybe I'm wrong.
When we put these videos into the custom video player, the videos play, but they do not rotate to the next video.  This is because, as I was told, the duration is not found in the metadata.  So I bring the question, am I using the wrong preset for this, or does the metadata not exist in the .mov file?  I'm unable to determine this, as I cannot even find the duration field in Bridge for either the .mov or .flv files.
There is my problem, if anyone has a suggestion or anything, please let me know.  I'm using the Production Premier CS5 suite.

Update:
After doing some more general searching about FLV duration metadata, I found that more people were having this problem and had to resort to metadata injunction techniques.  I, however, do not want to go through that because I'm lazy and want stuff done right the first time.  As a result, I've tested using F4V encoding from the original MOV files instead.  The metadata appears to be in tact, the player works as it should now and will have to go through and change the rest of my video files.

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