So I did some digging around and concluded that the "keep me signed in" issue is directly related to cookies. I found another working workstation and narrowed the sign-in process down to 5 different cookies (when accessing the URL for our domain.sharepoint.com site). As soon as I cleared these 5 cookies, I as-expected was forced to sign-in again however this time it is exhibiting the same behavior where I need to click my name to login.
What's interesting is this time the MSOL Sign In Assistant is not installed on the workstation, which I thought may had originally been an issue. I did sit down with some good old pen and paper and compare the old (working) cookies vs the new (broken) ones. I concluded that the new ones seem to be much more simplified and are missing a lot of identifiers. If it helps, the identifiers that I have missing across the 5 new cookies are:
WLOpt (I am missing fedjs=1 before credtype)
PPauth
cntrealm
RPSAuthTime
MSPVis
FedAuth
(One missing sharepoint.com at the end.....I was unable to read anything else in it)
PPLState
RPSTAuth
MSPAuth
MSPProf
Maybe it's just me but it looks like something possibly changed with the sign-in process or else the way the cookies are being encoded. Unfortunately it looks like cookies cannot be "tampered" with and I can't modify even the WLOpt one or the cookie deletes itself and recreates when accessing the portal.
I worked with MS support yesterday and we found out something interesting. We cleared out all Windows credentials in the password manager and cleared all IE temp files upon logging in everything went as expected. I closed and reopened IE and low and behold it logged me in automatically this time. Closed and reopened again and it was broken. They have my case escalated to tier 2 support currently.
Finally, I tried on a old WXP machine with IE8. It was not domain-joined (no GPO) but had the exact same issue where its requiring me to click on my name to login.
Hope this helps!
