Just wanted to say thanks for this. I was also a Lets Encrypt alpha participant and could never get past the login phase for Net7. I finally revisited this after a couple years and managed to also find this forum post. I found the same X1 cert in my Intermediate store. Deleting it and re-enabling CRL checking leaves me able to successfully log in.
Thanks again to any and all who helped contribute brain cells to troubleshooting this in some way.