ugh - talk about having to digg this... We run our internal certificate auth, so it was like moving from a commercial cert without an intermediate to one with one, keeping the private key.
This
post showed the solution...
I had not noticed that Firefox and IE both already had the intermediate, therefore I never noticed an issue there. However it was not in Thunderbird...
All the instructions on the wiki where based on creating a csr and key from scratch, or importing the root and intermediate certs.