I have two shipping profiles set up... one general profile for the majority of my items and one free shipping profile. When someone orders items from both profiles they aren't given the option of choosing the shipping service they'd like (i.e. First Class Mail or Priority Mail) for the item in the general profile. The cart only shows "shipping" as the only choice and provides the First Class rate. (although it doesn't inform the customer that it is the first class rate)
I still need the customer to be able to choose which shipping service they'd like even when they purchase products from both shipping profiles. How do I do that?
Yes the same thing is happening with our store! We would like our customers to chose the mail service they would like, instead of just "shipping", some customers want UPS or USPS Priority option to get their package faster than USPS First class mail.
Do you also offer flat rate shipping options? The reason I ask is because Shopify's shipping profile blending (this is when the rates combine at checkout) is based on name. You can customize the name of a weight or price-based rate, but not of a live shipping rate from a carrier. If there isn't a common name at checkout, it will take the lowest from each profile and blend them together with the title of "Shipping". Shopify explains this in their Help Center.
If you only have live rates in each profile, it can also be an issue of one product in a cart not meeting the criteria of a shipping service. I.e. some items may be too heavy to ship in an envelope, so that rate won't be triggered at checkout. Since the names no longer match, Shopify will combine the lowest shipping options and call them 'Shipping'.
If you're still experiencing incorrect naming and rates appearing, you've likely exhausted Shopify's shipping profiles of what they can do and need a third-party app such as Intuitive Shipping. Especially since you're using live rates, you can take advantage of our dimensional shipping algorithm to return accurate live rates at checkout - this gets you accuracy and the options you need displayed to your customers.