How can I match sound quality between video clips and audio clips?

Question

Hi guys,
First of all let me say that I enjoy using the latest Media Encoder. However, as a novice, I have two related problems.
1.I am recording video to use with PowerPoint slides in Adobe Captivate. I am encoding the video with best quality FLV. This produces very good video,
      but with a degraded audio track, even though I had filtered the audio in soundbooth. The post encoding sounds like it did before Soundbooth corrections.
2. Some of the video recording has been set cut into audio clips to be used as background narration behind PowerPoint. The logic behind this is: that if both are
      recorded at the same time, the voice quality should match.
This is far from the outcome. I have tried MP3 for the audio which of course produced the best sound- but is entirely unlike the rest of the video. I have also encoded the audio with Windows Waveform preset figuring that since the soundbooth edit was a .wav file, that there should be a reasonable match. Wrong again!
So, the audio quality of all clips is poor, and the difference between the encoded video clips, and the audio encoded clips spoils the otherwise professional result in Captivate.
Please help, all of you experts.

Answer 1

Thank you.
OS Windows 7 x 64; 3.2 MHz; 2 TB; 12 GB Ram-9GB ram allocated to Adobe.
My process is this:
1. The whole video and audio narration material is shot in one continuous video sesseion.
2. The microphone is only mono, but the camera is set to stereo. Noone can work out how to change the camera to mono.
3. In Premiere Pro 5, I select render and replace in SoundBooth.
4. In Soundbooth, I choose Add Multichannels.
5. In Multichannels, I delete the unwanted noisy channel, and any other unused channels.
6. With the remaining mono channel, I then select Export and Save As option, then Stereo.
7. Next I edit the stereo channels as needed.
8. The imported stereo won't automatically update in Premiere Pro, so in PPR I import the new edited stereo track.
9. I test this track in PPR, to check that it is playing R & L channels. It is. OK.
10 On the timeline, I proceed to cut apart this single stereo wavelength .
11.These clips are saved as Video, or Audio subclips.
12 From the video subclips, I export to Media Encoder, and choose either FLV4 match attributes (High Q). This I modify to custom 2 pass (Custom save).
     The summary says that this is saved to MP3 Stereo.
13. I import this into Captivate 5, but the Video outcome is Left channel only. I have tested this on Media Player/Real Player where it is also L channel only.
14. I export my Audio subclips to Media player, and select MP3 option and this summary also reports stereo. The Audio outcome is stereo, when played in any player and in Captivate 5.
I cannot understand how a single, continuous track edited uniformly in Soundbooth to stereo, can produce different outcomes in Media player.
I would so appreciate a solution to this problem, because, in the Captivate 5 e-learning production, the switch between stereo audio (behind PowerPoints), and l. channel video is distracting. Naturally, the l. channel only is a thin sound. It is as if it had never been edited in SoundBooth at all.