some printed ^M line ending text in Emacs after editing with Meld

[Karl Brand <k brand erasmusmc nl>]

Esteemed Meld devs & users,

What i do:

1. Create a script.r using Emacs/ESS.
2. Make some modifications to script.r by pulling some lines of code 
from another_script.r
3. Reopen script.r in Emacs/ESS to continue working.

All the lines in another_script.r which were *not* pushed to script.r 
end with ^M

Some times it's the other way around - only the line that was 
pushed/pulled ends with ^M's. So far i haven't isolated exactly which 
action determines where the ^M's are placed. Either way i still end up 
with ^M's all over the place and i'd like to avoid getting them after 
using Meld!

FWIW:
-all actions are performed under Linux (Ubunt 12.04)
-the directory is being synced by dropbox
-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 shouldn't be necessary and I'm hoping some one here can tell me 
how to avoid these.

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