FLV file not opening up in media encoder

I am on a unique job where we are trying to figure out our workflow for video live and on-demand production.  Basically, we will be streaming live video during the day and then we would then like to post the video that just went live and have it available in our on-demand archives.  For our on-demand, we have to have 3 different flv files at 3 different bitrates since we have no idea what our audience's individual computer/internet can handle.
Because we are doing a high volume of video for this job over the course of two weeks, I am trying to streamline our workflow so that my editors don't have to deal with long hours of babysitting a computer while it is encoding.  Because we have to go from injesting DV footage, then exporting QT, and compressor to make it a H.264 file since Media Encoder cannot read FCP QT files, and then into media encoder to make it to flv.  That is a lot of steps to be taking.  We also have lots of other things to edit aside from the live material.
We ourselves are sending out the video live on line, so permission is not an issue and we are not ripping off things off of big network websites at all.  You see, the video is encoding as it is going out and I found a way to record the flv video and maintain it in flv format.  However, we would just like to trim the heads and tails for the on-demand version as well create two other flv versions with a different bit rate.
For some reason, when I open the flv file that we recorded, media encoder does not see anything.  I took that same test flv file and put it in three different media players/compression software.  The flv opens in media streamclip, Adobe Media Player, and Sorensen Squeeze, so I don't understand why you don't see anything when it is in Media Encoder.
I was even able to trim and re-compress the recorded flv to a lower bitrate flv file.  I don't really want to use Sorensen because I tested versus Media Encoder and it is really slow compared to Media Encoder.  Can someone help me?
Thanks in advanced.
Michelle

I don't think that Adobe's Media Encoder can open FLV files at all, it only creates them.
Alternatively you can use some of the tools below to top & tail your videofiles:
- After Effects CS4
- Premiere CS4
- RichFLV (www.richapps.de)
Regarding workflow, have you looked into Adobe's Flash Media Encoding Server?

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