The shipping calculator will always return with a free shipping if you have a created a free custom or real time time shipping option. It will take precedence over the rest of the custom shipping options as research shows that free shipping is preferred.
To change this, you can either remove the free shipping option from your Shipping Settings or you can totally remove the shipping calculator as the shipping fee is always shown in the final amount during checkout process.
You could also change the wording from 'Free' on the shipping widget on the right hand side of the basket to something else (like, please contact us for a quote) by going to Settings>Store Settings, Language. Choose the language you are using and adjust the value to the right of the original value containing the words you are looking to replace (you can us CTR F normally to search for all those containing the word 'Free'). Then save.
