You're going to ask about two settings when I describe my problem, so let me say right away that I'm having a problem with URLs automatically hotlinking in my blog entries--ALL blogs, in fact on two hosts--and here are my settings for each blog:
Allow HTML in comments: NOT Checked
Auto-link URLs: CHECKED
(I reversed these settings in one blog, just to see if it makes a difference. it doesn't.)
I've tried really plain vanilla kosher URLS (e.g. http://www.talklikeapirate.com ), URLs without the protocol specified that have the www designator (www.google.com), etc. Nuttin'.
I would just ignore this and hot-link the URLs, as inconvenient as that is, but then I run into the problem that I mail out these entries with a Mailman list that converts the code to plain text. ... sigh ...
I did some searching on the MT site and didn't get anywhere, but if you're all shaking your head and saying you never saw this on DH, I'll go back and dig some more.