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User A needs access to a list. This list is already uninherited from the parent site.
I give User A read permissions, User A still cannot access list.
I add User A to a group with the same permissions (but also has permission to whole site), User A can access list.
Why is this? Is there something I'm missing? I am using the link directly to the list, so it should work, but user is given access denied until I add to specified group.
Chances are there are some elements on the page or master page which the user cannot access. Check the permissions for the group, what other permissions does the group have? Is your list using a lookup into another list (which that user would need read permission to as well).
You can also try running Fiddler to view the traffic requests when logged in as User A, see what is being called from where.
HTH
I have to add to this answer. Once I made sure that SharePoint Designer allowed my custom masterpage and viewed it as indeed a masterpage (was a blank Content Type), the permissions worked fine. Previously, the masterpage that I previously had whenever I opened this ticket was 'invalid' and SharePoint wanted me to change it. Once I created a new masterpage and copied over the changes from the old masterpage, saved it, published it, and approved it, the permissions per list worked correctly so that the user could have access to a list without having permission to the whole page. The previous masterpage said access denied to the specific list URL for the user that had read access.
