Actually I just looked at the source for the page that it's happening on and I suspect that it has something to do with the use of single quotes in the subject line of the message I received causing a parsing error with the html code for the reply button. If anyone wants to test it out I can send someone here a message with the same subject line as the one I received and couldn't reply to, I suspect the person I send the message to won't be able to reply to it either.
Source for "Reply" button for message where the button doesn't work:
<input type="button" value="Reply" onclick="location.href='sendmessage.php?to=247&subject=He 'who'???"e=6819'">
The first single quote in the subject that I have highlighted closes the single quote before sendmessage.