>I normally just use the .NET publishing wizard but that shouldn't make any difference. As I understand it ASP.NET makes a shadow copy of the /bin directory and uses this shadow copy to service requests. It also monitors the actual /bin folder for any file changes therein. When it detects a change it builds a new shadow copy. The existing copy is still used to service existing requests. New requests use the new shadow copy. When all existing requests are completed then the old shadow copy is discarded.
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>But, having said all that, I don't know why you should have the problems you are experiencing, or, by extension, what to suggest to fix it.....

I will let you know if I ever find the reason for all this.