I seem to be experiencing the same problem as mentioned in: http://requesttracker.8502.n7.nabble.com/RT-4-2-1-Weird-issue-with-HTML-comments-correspondense-RT-always-registers-plain-text-with-HTML-tags-td56005.html
I don’t have custom templates. The HTML tags are only appearing when replying through the web interface. Disabling the Rich Text Editor avoids this problem. Hope this can be fixed? Regards, .lzs