Admin Issues after Auto-upgrade to 4.1.1

After the upgrade to 4.1.1 can no longer login to wp-admin. Re-installing all the WP files except config and content fixes the issue until I logout and try to login again.

Anybody else experiencing this? What is strange is that this is only happening in sub-directory installations of WP – I have two of them and both are doing the same thing. I have numerous root directory installs and they appear to be normal.

Any advice on how to fix this or why it is happening would be much appreciated.