I have been desperately trying for the past few months to share my email on winodws and Linux using thunderbird. I normally dont use the "Local folders" for my email accounts in TB. I always create separate folder for all my accounts. I thought all I would have to do is create the initial setup in windows and then mount that folder from Linux and configure Linux TB to use the mounted directory. Some how it didnt succeed until I found this this URL:

http://www.pcquest.com/content/linux/2004/104050805.asp

One tip though: If on Linux you are using TB from a non root user you must make sure that the user has write access to the mounted windows directory.