I don't feel like reporting the bug to Oracle's issue tracker, they've always been slow at responding or providing any feedback regarding issues. If you feel like reporting the bug, feel free to do so. However, from your reply I understand that you already found out the cause of this issue. Why don't you patch the source code in the MariaDB tree and have this issue fixed in the next release?

Maybe we will, but we should report it to them anyway, for the sake of collaboration. I'll do that.
I didn't find the exact cause of the issue yet, I have some general suspicions, but it will require some more investigation. Apparently it has something to do with the interaction between syslog and the usual log, and possibly with the service or the way it starts mysqld_safe / mysqld, and with how they open logs.

I could reproduce it on MySQL 5.1 and 5.5 from the official repo (filed as http://bugs.mysql.com/bug.php?id=72598), but not on MySQL 5.6 from dotdeb repo. If it's not just the packaging difference, but the problem was actually fixed in 5.6, there's no chance it will be fixed in earlier versions, so we'll need to do it on our own anyway.

• install MySQL server from an official MariaDB repo (apt-get install mariadb-server);
• make sure that --syslog is enabled in the special config file;
• connect to the server and run FLUSH LOGS (works all right);
• add log-error=<path-to-file> to /etc/mysql/my.cnf, [mysqld] section;
• run /etc/init.d/mysql stop;
• if the <path-to-file> already exists, remove the file (it might be not necessary, but existence of the file seemed to affect the experiments somehow);
• run /etc/init.d/mysql start;
• connect to the server and run FLUSH LOGS (fails)

Is there some progress regarding this issue? I'm using 5.5.41 from MariaDB's official Debian repository and the issue still exists.