Using TB 220.127.116.11 I can send an email through my server, where it has domain keys sign it. On the receiving side, the keys verify.
Using Portable TB 18.104.22.168 (with and without GPG support) the email is sent, however the DomainKeys fail verification on the receiving side.
I am still working on a way to determine what is different as a visual look at the headers doesn't reveil anything.
Follow-Up: Upon further investigation, this is an issue with the domain keys package, and not thunderbird.