One of the tasks I faced in moving completely from Windows to Ubuntu was to transfer all my saved emails and my profile from Thunderbird. In Windows locate your Thunderbird profile, this will usually be in Documents and Settings>YourName>Application Data>Thunderbird>Profiles. The profile folder will be named with a random 8 character name and a .default extension (e.g. htg34gtd.default). You should be able to access your Windows partition from Ubuntu so once you’ve located the profile folder just copy it across to your Ubuntu partition.
Now go to your home folder in Ubuntu and select View>Show Hidden Files look for a folder named .mozilla-thunderbird. This may already have a .default folder in it, if it has then delete it then move the folder you copied from Windows here. Last thing you have to do is create a profiles.ini file in the .mozilla-thunderbird folder, in my case Thunderbird had already created this file so all I had to do was replace the text with below with the correct .default name;
Where oooooooo = the 8 character name of your folder.
Now run Thunderbird, all being well you should now see all your emails etc as they were in Windows. This was not the case for me however, Thunderbird decided to create a new profile .default folder but all I had to do was delete it and rename the one I copied across to the one Thunderbird created…voila!