identical variables have different SKUS

I just installed the plug in and have been having some trouble reaching a point where identical products get the same SKU.

When I change it manually, the SKU reverts back to the original.

We have listings with different colours. For example 1 listing is green t-shirt but when you enter the page, you can choose white, grey or green. Again another page called grey t-shirt will have white, grey and green option. These are all identical, I can not have them with different SKUS.