So we conducted another test and we found that the UID=0 is what's actually occurring here, but we're not sure why or how to change that.
Here's what we did to find this out:
We changed permissions to 755 on one user's home directory, and it allowed us to login without any Access Denied errors, but it's dropping us in the /root folder, which is indicative of the UID=0 (which is root).
Any idea why that might be happening? The logs I posted earlier show it occurring with Centrify, but my guess is it has to do with NSS or PAM like you mentioned before.
Also, I ran the adfixid command just out of curiosity, and it picked up 0 errors immediately - didn't really appear to scan at all...