Starting and Stopping FMLE from command line yields corrupt .flv files

I am using FMLE to record and live stream TV content. In order to this I am remotely calling FMLEcmd in order to start and stop encoding processes. The problem that I am running in to is that the .flv files generated are corrupt. The odd thing is that if I use the exact same profile XML from the GUI, then the encoding process works just fine and results appear as intended.
Here is the way my workflow works:
I start the process by calling
FMLEcmd /p C:\lighttpd\htdocs\xml\default.xml /l C:\lighttpd\htdocs\logs\log.txt
then at the conclusion of the recording I call
FMLEcmd /s "C:\lighttpd\htdocs\files\default.flv"
When I attempt to open the files using FFmpeg I get a codec error saying that no codecs were detected. When I attempt to open the files in VLC I get a error saying that the media types are "Undf". When I attempt to open or modify the files with flvtool2 I get an end-of-file error. My guess is that my stop command is incorrect and somehow abruptly stopping the stream, but I don't know another way to stop the stream. Do I need to specify a specific stream duration in the XML and make sure to call the stop command *after* the duration has been reached? What would cause this codec corruption when the same profile works properly from the GUI?
Here is the profile I am attempting to use.
<?xml version="1.0" encoding="UTF-16"?>
<flashmedialiveencoder_profile>
    <preset>
        <name>Custom</name>
        <description></description>
    </preset>
    <capture>
        <video>
        <device>Osprey-440 Video Device 1A</device>
        <crossbar_input>0</crossbar_input>
        <frame_rate>20.00</frame_rate>
        <size>
            <width>640</width>
            <height>480</height>
        </size>
        </video>
        <audio>
        <device>SigmaTel Audio</device>
        <crossbar_input>0</crossbar_input>
        <sample_rate>22050</sample_rate>
        <channels>1</channels>
        <input_volume>75</input_volume>
        </audio>
    </capture>
    <process>
        <video>
        <preserve_aspect></preserve_aspect>
        <deinterlace></deinterlace>
        </video>
    </process>
    <encode>
        <video>
        <format>VP6</format>
        <datarate>650;</datarate>
        <outputsize>640x480;</outputsize>
        <advanced>
            <keyframe_frequency>5 Seconds</keyframe_frequency>
            <quality>Best Quality - Lower Framerate</quality>
            <noise_reduction>None</noise_reduction>
            <datarate_window>Medium</datarate_window>
            <cpu_usage>Dedicated</cpu_usage>
        </advanced>
        <autoadjust>
            <enable>false</enable>
            <maxbuffersize>1</maxbuffersize>
            <dropframes>
            <enable>false</enable>
            </dropframes>
            <degradequality>
            <enable>false</enable>
            <minvideobitrate></minvideobitrate>
            <preservepfq>false</preservepfq>
            </degradequality>
        </autoadjust>
        </video>
        <audio>
        <format>MP3</format>
        <datarate>48</datarate>
        </audio>
    </encode>
    <restartinterval>
        <days></days>
        <hours></hours>
        <minutes></minutes>
    </restartinterval>
    <reconnectinterval>
        <attempts></attempts>
        <interval></interval>
    </reconnectinterval>
    <output>
        <file>
        <limitbysize>
            <enable>false</enable>
            <size>10</size>
        </limitbysize>
        <limitbyduration>
            <enable>false</enable>
            <hours>0</hours>
            <minutes>60</minutes>
        </limitbyduration>
        <path>C:\lighttpd\htdocs\files\default.flv</path>
        </file>
    </output>
    <metadata>
        <entry>
        <key>author</key>
        <value></value>
        </entry>
        <entry>
        <key>copyright</key>
        <value></value>
        </entry>
        <entry>
        <key>description</key>
        <value></value>
        </entry>
        <entry>
        <key>keywords</key>
        <value></value>
        </entry>
        <entry>
        <key>rating</key>
        <value></value>
        </entry>
        <entry>
        <key>title</key>
        <value></value>
        </entry>
    </metadata>
    <preview>
        <video>
        <input>
            <zoom>100%</zoom>
        </input>
        </video>
        <audio></audio>
    </preview>
    <log>
        <level>100</level>
        <directory>C:\Documents and Settings\Administrator\My Documents\My Videos</directory>
    </log>
</flashmedialiveencoder_profile>

If issue of corrupt file after cmd line not in GUI mode. Are you using some automation to copy/paste output flv to someother location?
AFAIK, after placing stop command, FMLE took some time to write proper EOF in FLV. wait ~10 sec for FMLE to complete file writing process and than play in FLV PLayer.
I tried manually with steps you mentioned and it's working fine for me.I playerd file in Applian Flash PLayer. "http://www.applian.com/flvplayer/"

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