Hi, I've found the best way to convert video(but time consuming and requires too many steps)
Tools: Flaskmpg(Xmpeg, Flaskmpg 0.59, Flaskmpg 6...any version)
Tmpgenc...any version
GraphEdit
Xmux
DVD player program like Cyberlink PowerDVD, etc.

1)First run flakmpg to see what AC3 stream you need(English, German, etc.) You will not convert it with Flaskmpg. I run flaskmpg just to find out the audio stream. For example, English audio stream shows up as second AC3 stream( 81,80,82, and so on) English is 80 so it is the second AC3 stream in this case.

2) Run Tmpgenc to encode video( Video ONLY. Do not use project wizard if audio is included in the wizard) Set up your video according to standard format. For example, SVCD is 480x480 29.97f. Again. don't do anything with audio. You will use GraphEdit to encode audio later. I found that GraphEdit can help you avoid video/audio synch problems.

3) When you're done with video, it's time to rip audio. Run GraphEdit.
Go to menu. Insert filters. Everything you need is under DirectShow by expanding it.

First filters. File source(Asyc) browse for your video source (not the one you just encoded)

Second filters(very important) use your DVD player filters like Cyberlink Vidio/Audio decoder) This filter will give you a list of one video source and many AC3 streams. Choose the one you need. Remember that in the first step English is in the second stream? So choose the right AC3.

Third filters WavDest

Four filters Filewriter(it will ask you to save your filename...this will be a WAV file which has not been downmix 48->44.1 for SVCD format) If you encode any format like DIVX this is o.k. don't worry about it.
Run the PLAY button it will gray out. When it's done, it will return to GREEN button.

4)Run tmpgenc again this time use Audio only) Set up your audio according to standard. For SVCD use 48->44.1 downmix and encode it as mpeg 1 layer 2. For DIVX don't downmix but encode it as Mpeg 1 layer 3 or mp3 as we know.

5)Finally multiplex your encoded video/audio with XMux or Tmpgenc.
In XMux you will have advantages of knowing the length of video and audio. If they matches, you will not have video/audio synch problems.
For example video length is 702 seconds and audio is 702 seconds. You certainly will not have synch problem. In Tmpgenc use mpg tool to multiplex it.

I believe XMux has some bugs. Sometimes muxed video has problems.
So try Tmpgenc if Xmux gives you problems.