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What are best practices for using msmq acknowledgements in an asp.net application?

In my case, some request from Flex to Asp.net (using WebORB or FluorineFX) adds an id to a queue. A windows service handles the queue to do a job with each id.

Now, after I added the id to the queue, I can't just wait until a message arrives in the acknowledgement queue. I'd rather add the id to a registry and let a background thread listen to the acknowledgement queue.

Is that a good way to approach the problem? I would need to start a background thread in the application start in global.asax. This background thread would be an infinite loop listening to the acknowledgement queue.

Another question is if this background thread forces the application pool to never die?