PayPal IPN not being processed in Joomla

Using Joomla 3.5 and above, the IPNs from PayPal Standard are not being processed. They are stored in the civicm_system_log table, but then an error happens:

[27-Jul-2016 16:10:25 America/New_York] PHP Warning: ini_set(): A session is active. You cannot change the session module's ini settings at this time in /.../libraries/joomla/session/handler/joomla.php on line 45

I was able to get around the problem by commenting out the following lines of code in civicrm/extern/ipn.php (around line 54):

try {
//CRM-18245
// if ($config->userFramework == 'Joomla')

{ // CRM_Utils_System::loadBootStrap(); // }

$paypalIPN->main();
}

I don't know if this should be a permanent fix, or if this causes some other problems down the line.