I have the same issue. I have WordPress hosted on GoDaddy. One install under root an one install under /wordpress.
All was working fine and from literally one minute to another I was not able to logon to the WP control panel under root. In a matter of fact I was automatically redirected to the WP control panel logon under the /wordpress install.
When calling up http://domain/wp-admin/wp-login.php I get the control panel logon screen, but it will not accept username or password. It was working fine for 2 days and today I just did a page content change and it took he first change but when I tried to submit the second change I was kicked out of the WP control panel and was not able to logon anymore. GoDaddy Tech support says that somehow the logon script could not read the WP DB and that it most likely was a permissions issue (????). So I changed the permissions for all directories to be read/write but no difference.
Right now I am reinstalling WP under root and see how long this will work.
