Sound and image quality of flash videos from video encoder

I have been using the articulate presenter pro '09 package for the past year and just recently upgraded to the '13 version.   I did not see an option to download a new video encoder and have already uninstalled my old version.  Where can I find this link?  

My main question though is about the sound and image quality.  I create a lot of video using movie maker.  These videos are formatted as an MP4 so to be able to use in presenter, I upload to the video encoder and publish as a flash file.  I've played around with bit rates and have used the calculator but I'm still unsure if I'm setting it up correctly.  I've also made sure the size is correct in both my movie maker and the flash player.  Should these two line up exactly with the bit rate settings?  

When I publish videos from my movie maker, they sound and look perfect, but when I convert them in video encoder, they come out much lower quality and sometimes cut in half or only show the beginning of the video.  I have also made sure to time the videos less than 8 minutes and the frames per second is also correct so what the heck am I doing wrong?

 Is there a best practice setting for audio/images created in MP4 (including voice narration, high res pictures and another for people moving and talking in a video?)  The calculator is a bit confusing to me and I'm not sure I have all the settings correct.

Is there another flash converter out there that works better (and free)?

Thank you!