Hmmmm...
A few more details might be a little more helpful... If you could write a scaled down version of your program that demonstrates the problem, that would be helpful for anyone trying to solve your problem.
I wish I could help you as I'm also doing some stuff with the HTTP server, but I'm just starting and don't have much experience with it.
One that comes to my mind is:
When is the webserver activated? You can programatically engage the webserver once your dynamic http vi is run, and disengage it when that VI is shut.
(This may have been the first thing you've tried and be thinking "thank you captain obvious" - in which case I apologize. Sometimes it's hard to judge the level of experience of the user from their posts. I reiterate that if you
provide a sample VI that can reproduce the problem, it could go a long way towards solving your problem)