Recently, I'm seeing DOS line ends, ^M, on my /var/log/boot.log file. Honestly, I don't check this very often so I can't say exactly when this occurred. Is this just MY experience or are others seeing this also.
I checked a C6 /var/log/boot.log from 5 years ago and ^M chars are there all right. You can easily spot them with less -R /var/log/boot.log. This is a surprise indeed and it's not configurable. Try to comment out echo -ne "\r" lines in /etc/rc.d/init.d/functions if you hate the output so much.