I have installed phpMyAdmin on my Linux CentOS 6 for quite some time.
I had double secured it with .htaccess file in /usr/share/phpMyAdmin
And I have suitably modified /etc/httpd/conf.d/phpMyAdmin.conf like this:
Allow from all
I regularly do yum update and after my phpMyAdmin upgraded to 3.5.3, this password protection stopped working and NOT ONLY That but it also causes, phpMyAdmin not opening until, you delete .htaccess file from /usr/share/phpMyAdmin
I feel insecure without having .htaccess protection.
Other relevant details are as under:
OS CentOS 6 64 bit architecture
PHP version 5.3.3
My SQL Version 5.1.61
PhpMyAdmin Version 3.5.3