See http://kb.mozillazine.org/Move_to_a_new_PC#Moving_from_Windows_to_OSX_or_Linux

I'm trying to move from linux to linux so not sure if that article is relevant to me. However, I tried running Thunderbird from the command line with the -profile option, but this did not help; I'm still seeing only the one email account, no local folders and am not being prompted for the master profile.

Hi Joolsmy. The original method you tried of copying the .thunderbird folder should have worked. Could explain what you experienced when you say "Thunderbird was not able to access the profile"?

Right now, I suspect you had Thunderbird running at the time you copied the folder from your original computer. Make sure Thunderbird is not running when you move your data.

Hi Chris, Turns out I've been a bit stupid. I had forgotten I had already moved the profile on the original pc and it wasn't in the .thunderbird directory, but there was an old profile there which was the one I was trying to use.

I only realised when I checked the profile.ini and saw the modified path. Now I've transferred the right profile it's all working perfectly.

Thank you for helping and sorry for the confusion.