AFAIK screen -ls considers a screen session dead at least when the server crashed but the socket is still there.
I wonder if the opposite ("SCREEN" server still there as your ps output shows, but the socket is gone) could be a reason, too, i.e. if the move from /var/run to /run could be the cause. (Just an idea which should be checked. Will test that. :-)
AFAIK screen -ls considers a screen session dead at least when the server crashed but the socket is still there.
I wonder if the opposite ("SCREEN" server still there as your ps output shows, but the socket is gone) could be a reason, too, i.e. if the move from /var/run to /run could be the cause. (Just an idea which should be checked. Will test that. :-)