As Anonymous Monk, remarked cygwin and windows don't have the same concept of home.

In the past I've had ActiveState perl and cygwin perl coexist. You problem never cropped up. I used a different home directory for cygwin something like /home/myself (equivalent to /cygdrive/c//home/myself). While my motivation wasn't to get the 2 perls to coexist in peace, this approach could work for you.