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No, it's caused by Joomla!. IIRC, it happens only on Joomla! 1.5. Sometime around 1.6 or 1.7 (I don't remember exactly) this behaviour was considered a bug and got fixed.

Since this is not an issue with my software I would rather not reply. The simple reason being that I have no idea about your site and server setup and my reply could be wrong. I can only provide accurate support for the software I've built and know how it works. I think the best approach in your case would be raising this question in the official Joomla! forum.

IMHO, it's a bug.

0444 means: owner user has read permissions, owner group has read permissions, everybody else has read permissions.

0644 means: owner user has read and write permissions, owner group has read permissions, everybody else has read permissions.

Both permissions allow EVERYBODY to read the contents of configuration.php. Depending on your server configuration this is a feature (shared craphosts) or a glaring security hole (properly set up server with isolated users). The first set of permissions doesn't allow the site owner to edit the configuration while the second allows him to do it. In other words 0444 permissions deal with no security issue whatsoever. No hacker will write to the configuration.php file (it's stupid and futile). They will instead read it so that they can get access to your database (= modify your content = profit for the hacker/spammer!) or even get access to your FTP account (= full access to your site's files = spam static HTML pages = really effin' huge profit).

So, no, 0444 permissions is not a feature. It's a bug introduced by those who think they understand web security. Secure permissions would be 0600 but only if the site was running under a dedicated user, e.g. suPHP or mod_itk was in use. Otherwise the permissions should be left alone and the site owner should decide what's the best combination. Simple and secure.

You are getting timeout errors, most likely because your database takes an exorbitant amount of time to respond. You can either try fixing it yourself using phpMyAdmin or ask your host to run a check and optimise on your database tables. I'd recommend asking your host to do that for you.

Please ask your host for support with this issue. As I told you you are getting a timeout error. I can't help you with that. Only someone with administrator (root) privileges on your server and who's familiar with the server's setup can possibly help you.