Cygwin64 installed while MKS Toolkit was present

Question

Has anyone done this and what was the result? I did this after turning off MKS at the service level. However, after doing all of the steps to install cygwin64 it now opens with the windows command prompt instead of the cygwin shell. I have tried everything I can find to set this correctly but nothing has worked. It defaults to C:/users/whatever. I did not get the home directory after opening cygwin.bat I can run cygwin but it uses CMD prompt controls and that is not really acceptable. I tried copying .bashrc to the home folder it gave me and all I get is ~ as the home I made a correct C:/cygwin64/home/user directory and put all the needed files in place such as .bashrc and .bashrc_profile etc. but I still do not get what is needed. Uninstalled MKS and reinstalled cygwin and it made no difference. Looking for some advice or pointers if any. I looked at ../etc/nsswitch.conf and it looks the same as all of the good cygwin installs I have done. I tried deleting the user environment variable HOME and no change. I aimed that variable to the c:cygwin64/home/user folder and no change. My system environment variable match exactly to how I have them on a good install. when i source .bashrc it does not find it.