Even if your files use a DVD-Compatible codec, there is another reason for horribly slow encoding. Microsoft DVD Maker's encode process runs as a background process at a low priority. All this means is that, it'll run slower than anything else on your computer, whether that be AIM, Weather Bug, what have you.
If you need to encode fast, and don't mind it dramatically slowing down your computer for a much shorter amount of time read my article on how to speed it up (
Windows DVD Maker: Encoding Slow)
For the savvy, just use the task manager to change the priority to anything other than normal

.
Hope this helps,
Jeffrey