In my case on Win2008R2 MSMQ successfully received message from configured website in IIS 2.0( Integrated mode) but with in 1-2 minutes all the messages being disappears from MSMQ, this is not clear why ?
I have also tried to debug the same process using visual studio and through VS web server created message in MSMQ are still there on Windows 8.1 system which is OK.
So in our case only having issue with message received from website (IIS 2.0) and these are being disappearing.
The issue has been resolved by using below Code:
IIS Settings need not be changed, it was a code issue.
// Peek and format the message.
msgQueue.Formatter = new BinaryMessageFormatter();
Message myMessage = msgQueue.Peek(new TimeSpan(0, 0, 3));
MailMessage mailMessage = (myMessage.Body as SerializeableMailMessage).GetMailMessage();
if (SendMail(mailMessage))
{
msgQueue.Receive();
}