Have you saved the changes in the shipping settings, after adding the base rates?
You can resolve this by deleting the shipping method you had set up before, and then create a new shipping method under the shipping and delivery section of the settings, under that new shipping profile, choose the manage rates and add rates as per your choice and create conditions under that, shipping charges is applicable to all products.
I'm Miles from the Social Care team at Shopify. It sounds like there's an issue with the setup of your shipping rates. I'll walk you through some checks you do in your shipping settings. If these don't work, I'll also leave you details on how you can contact our team.
First up, let's have a look at how you've set up shipping rates. If you head over to Shipping > Settings, you'll be presented with an option to manage your rates. If you click "manage rates", take a look at your zones. Have you set up shipping for all countries, regions and states you ship to? If not, you can add a new zone by clicking "create shipping zone". From there, select the countries and regions you'd like to ship to. You'll then be able to add your shipping rates.
You also may have set up conditional shipping rates. As an example, you might want to provide free shipping for orders over $50 and charge $x for anything below. If you have conditional shipping set up, be sure to check those conditions out to make sure you haven't set them up incorrectly.
My recommendation is to take a look at our guide on setting up shipping rates and setting up shipping zones to see if that helps solve any issues. If not, it looks like we’ll need to access your account in order to resolve this issue. While we’re not able to provide account-specific support via the Shopify Community at this time, we’d be happy to continue assisting you through live chat, email, or callback. Please visit https://bit.ly/3cJkx8V and log in to your account to create a support request.