Hi,
Good news.
I actually didn't notice you giving me location of the certs earlier. I compared it now and found the fault.
The issue was in permissions. I had
ls -lah /home/username/ | grep pki
drw-r--r-- 3 username username 4.0K Apr 27 2017 .pki
I did
chmod -R 700 /home/username/.pki/
ls -lah /home/username/ | grep pki
drwx------ 3 username username 4.0K Apr 27 2017 .pki
Which fixed the issue.
Thank you for thorough investigation.