It happened to me with a previous 3.1x Thunderbird version. Maybe upgrade to 3.1.9. Might be some setting in html composing settings, or , I also noticed a boost when unmarked global index and search checkbox at Preferences/Advanced , General tab. Other things I did not try (as an update solved it) were deactivate grammar auto checking, use only non html composing, etc.
It might be that you have it configured as typing in text only mode, but there's a setting at composing settings, in preferences which give you several options, and default I think is type in html, rich format, if the original wrtitter was doing so. So would happen only in replies, not in a new blank message.