First, let's determine which part of the process decided to poop its pants.
Do you still have the original file that you ripped from the DVD? Play it - is the audio off there? If so, then you just need to re-rip the footage. When you do, make sure that the "re-sample audio to 48k" is checked if it wasn't on your first try (I've had that button cause me some grief in the past).
If not, go one step further down the stream. Play the file that the converter created. The file that's on your hard-drive, not the one online. If the converter caused the problem...try re-encoding. I've never actually used that software, so I'm not sure what else you could do to fix it inside the application. I'm not terribly familiar with Windows-based solutions, but if your converter keeps failing QuickTime Pro should do the trick (~$29, I think).
If there's no lag from the transcode, then somehow the YouTube Flash conversion (what happens when you upload a video to YouTube) introduced the problem.
Also, from Squared5 you should be able to create a file that is YouTube appropriate directly, without having to use any intermediaries. Just choose the Quicktime option, set your encoder to H.264 and your frame-size to 480x360. YouTube servers are pretty robust, and can handle just about anything you throw at it (quality, obviously, will vary).
Let me know if you need anything else!