Problem Encoding WMV to FLV with Media Encoder CS4 (but not with CS3)

Hello,
I have been attempting to encode some WMV files with Flash Media Encoder CS4 (I have Adobe Creative Suite CS4 installed) but it has failed, generating this error:
- Source File: C:\Documents and Settings\usf\Desktop\incoming\ch01.wmv
- Output File: C:\Documents and Settings\usf\Desktop\incoming\ch01_3.flv
- Preset Used: Custom
- Video: 624x343, Same as source [fps]
- Audio: MPEG Layer III (MP3), 128 [kbps], Stereo
- Bitrate: VBR, 400.00 [kbps]
- Encoding Time: 00:06:36
5/28/2010 11:26:16 AM : Encoding Failed
Error compiling movie.
Unknown error.
On another computer where Adobe Media Encoder CS3 is installed (with Creative Suite CS3), I experience no such problem. I do notice that when I add the WMV to Adobe Media Encoder CS3, it opens a window that prompts me to use "ffdshow", which will apparently work if it's configured to decode the file. I click "OK" and start the queue in the encoder. A few minutes later I get a successfully encoded FLV file.
I have come to question whether Adobe Media Encoder CS4 should be re-installed, whether the entire Suite should re-installed, or if there is some patch or fix I can install somewhere. Adobe Media Encoder CS4 is installed on my "production" computer which also has Adobe Premiere Pro (CS3) and Adobe Premiere Elements (7).
Could use some advice here.
Glen
P.S. the files will also not export to FLV using Adobe Premiere or Premiere elements...

Again, the reason we are capturing with Windows Media Encoder is because we tried using Live Flash Encoder to capture directly into flash but our equipment wasn't fast enough and it was dropping frames all over the place. We also don't have the space to capture into an uncompressed format because we don't have the available storage, and our events can be 8 hours long or more (each video is about 15 minutes, 20 or more videos)
Ive listened to everything in my workflow and it sounds fine until the outputted FLV file from AME.
WME is capturing at the following specs:
160kbps 48KHz Windows Media Audio 9.2 codec (stereo) 1 pass CBR
1800kbps 1 pass CBR video
29.97 fps
640x360 resolution
buffer size: 5 seconds
key frame interval: 8 seconds
I have verified this with a codec info utility I ran on the wmv files.
AME is encoding with the following specs:
FLV Multiplexing
On2 VP6 codec
620x360 resolution
800kbps 2 pass VBR
100% undershoot at best quality
160kbps stereo MP3 audio
I verified the above with the same codec info utility (gspot 2.70a) and it is all acurate, it also told me that the audio is at 44.1KHz rather than 48 (there was no place to specify this, is this a limitatino of the VP6 codec?)
Yes, these are our source assets. They're being captured either through an XL2 via firewire, or from an analog program feed converted to firewire via a Canopus converter box.
If anyone has any suggestions on how to get rid of this, or a different encoder (either to capture with rather low cpu resources, or to encode into flash) let me know. I can provide a sample of the clipping if you need
Thanks,
Peter

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Audio
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