Whew, after a bit of debugging I found the cookie issue with builds >1008 – and it was all my fault – my apologies!
I finally noticed in the changes from 1008 to 1009, that pluggable.php changed the functions that set the cookies. Then I had a sudden recall where I made an auto-load plugin to force year-long cookies (_cookie-year.php) which was now interfering with the function. Deleting the plugin allowed the logins to work.
So anyone that happens to be using _cookie-year.php will have to replace it when I get time to make an update.