Is your shipping weight based?
If I leave a value out of my weight field then my shopping cart ignores the P&P formula and charges £0 for shipping ... there might be a way to fool your cart.
That said I had a similar nightmare to start with as I'd chosen value based shipping when I first started out and needed to change to weight based which meant working through my product manager and adding a weight value.
If you post which shopping cart or shop package you are using some one might know how to get round it to save you having to spend so much time changing things ... I'll keep my fingers crossed for you
