I'll see what I can do to fix this (since I originally did the hack
about -igncr when invokig the bash shell) ...
I've committed an (ugly) hack in SVN #31538 which fixes the problem for
win-setup.sh.
(Although not currently a problem for the Wireshark Windows build, the
real issue is not fixed.
That is: once cygwin bash is invoked with -o igncr all further
sub-shells should also run with the -o igncr option. This apparently
requires doing things differently than is currently done.
For all the boring ugly details see
http://www.mail-archive.com/cygwin-announce@xxxxxxxxxx/msg01711.html)
