Hi,
I have the same problem. I have the mysql 5.6.x and when I create a new database in CWP and then I try to access via phpmyadmin I get this error "#1045 Cannot log in to the MySQL server" even if I create a new user in CWP the problem still happen.
Thank you
Update 04/06/2016
I found a solution for this. In my case what I do is:
Backup all databases and then :
Via ssh
mysql_upgrade -u "your mysql root user here" -p
When the upgrade process finish delete and create again the account in CWP. Login in the account go to phpmyadmin and login again and now is working.
I think something is messed up after the mysql upgrade to 5.6.x.
Sorry for my english.