Enabling LDAP via samba, krb5 and sssd breaks glassfish

I have recently enabled ldap authentication using the procedure in the admin guide https://access.redhat.com/documentation/en-US/Red_Hat_Enterprise_Linux/6/html/Deployment_Guide/ad2008-example.html
The problem is that an application that I my glassfish service cannot be stopped or restarted using the normal gf start or gf stop commands whether as root or gfadmin. The only way to kill it is using kill -9.
I suspect that sssd and pam are somehow to blame, but I'm not exactly sure where to begin troubleshooting this.