3-Tier Connection for Admin work - Any known issues? - Windows Authentication

Hello fellow admins, 

I have been running into some odd behaviors with my new environment using Windows Authentication. 

In order to login to the Clients using a SQL Worker AD account we needed to configure the 3-tier connection that uses the Cherwell IIS Application pool - CherwellAppServer. All the Cherwell IIS Application Pools then have the SQL Worker Account set as the Identity. 

Some of the odd stuff i have seen so far is scanning a blueprint will complete, but never pop up the prompt at the end letting you know there was no errors. It does come up sometimes, but not all the time. 

Other odd stuff includes when i am in a blueprint and clicking on some of the managers from the menu (ie One-Step Manager) i can click on it and nothing happens. Log out of the client and back in, then it works. 

Some of these odd things make it seem like a 3-tier connection issue. Just not sure if its that or a deeper setting that others have ran into . 

Looking for help. Let me know.