First, I've found that the Sansa prefers ID3v2 over v1.
Secondly, it seems to handle MP3 tags better than WMA tags.
The only time I ran into a problem with list order was with an audiobook in wma format. The fix was to transfer in MTP mode rather than MSC mode. I usually use MSC mode as it is much easier and faster. I find that MTP mode in Media Center is excrutiatingly slow on my system. But, MTP mode did fix my track order problem.
The other problem I have with MTP mode and Media Center is that MC does not honor the folder structure stated in Handheld options. I transferred an audiobook today and it put the first file in the root of the Sansa and put the rest of the files in a hidden folder named ~music (or something like that with the ~ symbol, I deleted it and moved the files into the correct folder).