After doing a bit of googling around, it looks to me like PHP wasn't compiled correctly. If you read through the Snort document I pointed you towards, you'll see that PHP needs to be configured at compile time to point to the MySQL directory. The flag would look something like --with-mysql=/path/to/mysql
Now from your phpinfo dump:
It looks to me like PHP is looking in the /usr directory for MySQL. If that isn't where MySQL actually lives, that could explain why phpmyadmin isn't finding the right files.
If I were in your shoes I would compile PHP from scratch. The Snort document points to sites that should solve the dependency problems.