How to avoid the ^M induced by Meld and Git

Esteemed Git users,

What i do:

1. Create a script.r using Emacs/ESS.
2. Make some modifications to script.r with the nice diff gui, Meld
3. Commit these modifications using git commit -am "my message"
4. Reopen script.r in Emacs/ESS to continue working.

The lines added (&/edited ?) using Meld all end with ^M which i 
certainly don't want. Lines not added/edited with Meld do NOT end with ^M.

There are plenty of posts around about these being line endings used for 
windows which can appear when working on a script under a *nix OS which 
has previously been edited in a Windows OS. This is not the case here - 
everything is taking place on Ubuntu 12.04.

FWIW: the directory is being synced by dropbox; and in Meld, Preferences 
 > Encoding tab, "utf8" is entered in the text box.

Current work around is running in a terminal: dos2unix /path/to/script.r 
which strips the ^M's

But this just shouldn't be necessary and I'd really appreciate the 
reflections & advice on how to stop inducing these ^M's !

With thanks,

Karl

(re)posted here as suggested off topic at SO:
http://stackoverflow.com/questions/13799631/create-script-r-in-emacs-modify-with-meld-git-commit-reopen-in-emacs-m

-- 
Karl Brand
Dept of Cardiology and Dept of Bioinformatics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
T +31 (0)10 703 2460 |M +31 (0)642 777 268 |F +31 (0)10 704 4161