Percona Server - binlog not automatically purge with mysqladmin flush-logs
Please note Paragraphs 2,3 in the MySQL Documentation for binlog_expire_logs_seconds:


  The default binary log expiration period is 2592000 seconds, which equals 30 days (30*24*60*60 seconds). The default applies if neither binlog_expire_logs_seconds nor the deprecated system variable expire_logs_days has a value set at startup. If a non-zero value for one of the variables binlog_expire_logs_seconds or expire_logs_days is set at startup, this value is used as the binary log expiration period. If a non-zero value for both of those variables is set at startup, the value for binlog_expire_logs_seconds is used as the binary log expiration period, and the value for expire_logs_days is ignored with a warning message.
  
  To disable automatic purging of the binary log, specify a value of 0 explicitly for binlog_expire_logs_seconds, and do not specify a value for expire_logs_days. For compatibility with earlier releases, automatic purging is also disabled if you specify a value of 0 explicitly for expire_logs_days and do not specify a value for binlog_expire_logs_seconds. In that case, the default for binlog_expire_logs_seconds is not applied.


Please review your my.cnf

If you have this line in the my.cnf

expire_logs_days = 0


change it to

expire_logs_days = 1


Then go execute

mysql&gt; SET GLOBAL expire_logs_days = 1;
mysql&gt; FLUSH BINARY LOGS;


This will cause a new thread to be opened with the new setting.

It's OK to have 

expire_logs_days = 1
binlog_expire_logs_seconds = 86400


because the documentation says when both are set, binlog_expire_logs_seconds will take precedence and a simple warning is posted for expire_logs_days.

As a last resort, please restart mysql

service mysql restart


If you still have a problem after doing this, then I would suspect a bug.