Does this apply to all your mail folders? Or only the folders you opened in Linux? It's possible that by opening them in Linux, and especially if you made changes, you might have corrupted the folder indexes: that's a common cause of blank messages. Other possible causes, and remedies, are suggested here: http://kb.mozillazine.org/Disappearing_mail

PS did you read through this article when you set up Thunderbird to work across Windows and Ubuntu? http://kb.mozillazine.org/Sharing_a_profile_between_Windows_and_Linux There are important issues about file system compatibility. Also (at the end) it mentions a problem that can arise when Windows hibernates rather than shuts down properly.

Sorry for the very late reply and thank you for your help.

I had read the article and followed it through so all was well for a while.

I think my problems started when I ran Thunderbird in Linux and the Windoze partition containing the mail folders was not mounted at the time ( it's mounted at boot now to prevent this happening again ). I suspect I didn't follow the instructions properly on the second set up after this.

I still have some corrupted mail but I have learned a lesson :-)