[ESS] ess-mode 5.3.5; M-x R messes up RET in new shells

[Tim Hesterberg]

I normally run shells within emacs, on Windows, using bash (from Cygwin).
Running
	M-x R
changes something so that new shells do not work; an additional
newline character gets appended that bash doesn't know to strip off, e.g.:

$ pwd
bash: $'pwd\r': command not found

Anyone know a fix?

Does anyone know how to compare two buffers, to see what local emacs
variables differ between them?
I could use that to see what variables differ between
* a shell that works (started before M-x R)
* a shell that doesn't (started after M-x R).

Thanks
Tim Hesterberg

--------------------------------------------------
Details:
I start a new shell using M-x shell.
Normally I can start multiple shells by killing or renaming the current
shell buffer *shell*.
But after doing M-x R, any new shells no longer work, for most commands,
apparently because an extra character is getting pasted on (or conversely,
no longer removed).  I suspect this has to do with different end-of-line
sequences under Windows compared to Linux.

Here's another symptom; there seem to be two eol characters sent to
the process; I can use \ to remove one of them:
$ echo "a" \
a 
$ pwd \
/cygdrive/h
$


Running either of these doesn't cause the problem:
	M-x splus80
	M-x stata
(caveat - I don't have Stata installed).

This does cause the problem
	M-x R  (but kill when ESS prompts for the data directory)
This indicates that the problem is at the emacs level rather than the R level.

I have reproduced this an an emacs started with -no-init-file 
to avoid my .emacs
I'm using ess-mode 5.3.5.
When I installed Cygwin, I accepted the option to use Unix eol sequences.