We having been using PayPal IPN Handler to deal with payments from our website, however recently we have ben getting messages saying they are failing.  The odd thing is the code from our side is running, we are getting these notifications, we are processsing the payments and we are firing off email.  The last step of our IPN handler is to fire off an email and this does indeed work.  Once this email has been sent the PHP code does a 

header("HTTP/1.1 200 OK");

 to say its all good.  The only reason i can see that this wouldnt be fine is if the headers had already been modified or something, i added a 

if ( headers_sent($filename, $linenum) )
{
file_put_contents(__DIR__ . "/headers.txt", "FILE: " . $filename . " LINE: " . $linenum);
}

to log if this was the case but this doesnt trigger.

This is code that hasnt changed and im at a loss to how to debug it?  Any suggestions would be great as this is a busy time for us and PayPal have now disabled the IPN