Popping sounds when transcoding wmv to flv with media encoder

Whenever I use adobe media to transcode a wmv file created in windows media encoder to a flash file, I get pops  in the audio track (similar to hissing bacon). The pops only occur during the begining of the video, when it's quiet and go away once the music or any loud noises begin. I did some research and found that it's a common problem when changing sample rates but the thing is that it doesn't happen on every conversion, and happens across multiple computers. We've tried it on Dell precision m65s (xp pro) as well as a Dell xps (vista 64bit) and a MacBook pro running xp pro in bootcamp. Here are the settings we use in windows media encoder: 1800kbps video 160kbps CBR audio at 48khz 640x360 resolution 29.97 fps keyframe: 8 seconds  And here are the settings we use in AME: flv multiplexing on2 vp6 codec 2 pass vbr at 800kbps "undershoot" at 100% (quality: best) mp3 audio at 160 Kbps we have found that these settings work best for our cdm (brightcove)   Again, it only happens at the begining of a video when it is quiet. Does anyone have any idea what could be causing this? Before anyone asks, the reason we don't capture it directly into flash with live flash media encoder is because the motion in our content causes the processor to peak resulting in dropped frames. When we get better equipment we will switch to live flash media encoder but until then we are stuck with windows media encoder.  Thanks, Peter

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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