I also have this problem. I created a full backup of a fully working site with Akeeba and plavced the JPA in a new sub folder. When I then use kickstart to install the JPA, when I visit the site front end I see:
Install and activate Helix Ultimate Framework.
If I try to login to /administator of the subfolder, I see the login panel but on adding the correct credentials I see :
Warning
JAuthentication: :authenticate: Failed to load plugin: plgauthenticationjoomla
JAuthentication: :authenticate: Failed to load plugin: plgauthenticationcookie
JAuthentication: :authenticate: Failed to load plugin: plgauthenticationwatchfulsso
Logging into admin fails.
Advice please?