What you need to know?
Locations of the Profiles in Windows and Linux
On Windows its located in: "C:\Documents and Settings\UserName\Application Data\Thunderbird\Profiles\randomprofileid.default"
On Linux: ~/.mozilla-thunderbird
There is absolutely no need to copy your mails from windows to Linux partition. You can keep them where they are incase you do not plan to uninstall ur Windows OS or you frequently toggle between both OS like I do due to work requirements.
So here is what you do either copy your randomprofileid.default folder to the Linux partition or link it inside the ~/.mozilla-thunderbird folder.
Here is how you link it:
ln -s /media/WinPartition/Documents\ and\ Settings/Albuquerque/Application\ Data/Thunderbird/Profiles/okapp5e4.default/ ~/.mozilla-thunderbird/okapp5e4.default
Now you need to edit the profiles.ini file located at ~/.mozilla-thunderbird/profiles.ini
Here is the snippet from my Modified Profile
I added the new Profile 1 section in place and added the path to point to the one which is the one i linked above. Also changed StartWithLastProfile=1 to StartWithLastProfile=0 so that I would get a choice at startup.
Now start you firefox and you are done. Enjoy ur mails on both OS without any problems.