I am currently having an issue where customers on my site are checking out with products only to see that there shipping isn't available in their region. Our site currently ships to Canada and the USA (with some exceptions). However, for certain vendors on our site, when products are selected and added to cart, the checkout page says that products cannot be shipped to their location (even if it is somewhere we ship to). We deal with 4 main vendors, each of which operate their own warehouse. I have added each product by vendor to their own Shipping Profiles and set up rates. However, while these products are in their Shipping Profiles, customers are unable to checkout and choose shipping options. Yet, when I remove the shipping profiles and use "General Rates" all products work fine. We do not currently track shipping on our site (all products say "do not track inventory"). Is there a way I can mass stock each product by vendor for their warehouse locations? I believe the issue is that while the products are in their own Shipping Profiles, they are not stocked for those locations, and so they do not show the right shipping options at check out.
From what you're describing, Profiles should work for your setup.
I can think of two potential issues that are causing this:
I hope this helps!!