>I don't know how you are managing connections or what SQL operations takes place at startup (or shutdown-see below) but, normally, I wouldn't think SQL should be a problem...

A connection is opened at every hit. It is closed in the EndRequest() method.

>Given that the new instance kicks in so quickly then that sounds as if the process that you are killing is the 'old' instance and that it is not shutting down properly. But that, in itself, shouldn't prevent the new instance from running since, by definition, it has to take over the acceptance of new requests to allow the old instance to become idle. Maybe some sort of deadly embrace : the old one can't shut down because the new one is locking some resource and the new one can't complete initializing because the old one is doing the same? Again all just supposition (and getting a bit esoteric).
>
>I'd really suggest putting logging code into the Application startup and shutdown events so that you can get a clearer picture of what is happening ( maybe give the instance a Guid on startup so that you can differentiate between the two instances)

I am not sure what you mean by shutdown events. I have code in the Initialize() method which is executed on the first hit. Then, on each hit, I open and close the connection. But, there is no shutdown code.