Its saying products have been modified but the plugin is not updating/modifying my products?

For this plugin to pickup on variations they have to be added correctly in the first place. Woocommerce variations should first be created in the attributes section, then added to products.

Here is the step by step process.

1.) Go to Woocommerce > Attributes

2.) Create your attribute (Color)

3.) Click the “configure terms” icon to add terms/variations to your attribute (Red, Black, Blue, White)

4.) Once you have added all your variations, go to your product, select “Variable Product” for product data.

5.) Go to Attributes and select the attribute(s) you created (T-Shirts) from the drop down, click add.

6.) Click the button “select all” to add all variations to the attribute.

7.) Check the box “used for variations” and “show on product page” then click “Save Attributes”

8.) Go to Variations and click the button “Link All Variations” and it will automatically add all variations to your product. Or you can select them individually.