Your previous cygwin.bat file had options in it that meant that bash ignored the .bashrc file. This was really annoying as it took me forever to work out why. The new cygwin.bat file is as follows:-
start rxvt -sr -sl 10000 -fg white -bg black -fn 13x22 -fb 13x22 -tn cygwin -e /bin/bash
--login - to the end of the last line results the config file being ignored. One day I will read the manual.