I am under Lubuntu 12.10 with thunderbird 16.0.2
When I send a pdf file, people who receive it cannot open this pdf with acrobat or evince. It appears that in the source of the mail, thunderbird said that my pdf file is a plain/text file instead of a binary or a pdf file.
I look at this http://kb.mozillazine.org/Send_plain_text_attachments_as_real_attachments but it does not solve my problem.
Check if attached .pdf files are automatically opened with e.g. Acrobat when clicking on an attachment (by opening your Thunderbird's preferences).
For me, the problem occurred as soon as I determined to not to be asked anymore what application I want the .pdf to be opened with. All outgoing mails immediately stopped having proper .pdf's attached.
I reset it to "ask me" and .pdf's are .pdf's again...