It's Windows Authentication.
1. Set IIS to use Windows Authentication, disable all other authentication types
2. Edit ~/App_Data/hapConfig.xml, on the AD node, set AuthMode="Windows"
This should make HAP+ work in Windows Authentication Mode
You will need to configure HAP+ again using the basics, a fair few settings have been changed which the upgrade script would of changed, but obviously it doesn't work sometimes. Sorry to say :-(
You will need to backup your hapConfig.xml file, delete it and create a new one, sorry, there was an issue with the v8->v9 upgrade script that I wasn't able to figure out