I've had a similar issue. I'm on a 14-day trial for Product Levels. I started by setting up a new Variable Product, and then created new Product Part White and Product Part Black. I added the White and Black to my Variable Product, along with some inventory stock numbers for Black=13 and White=16. Everything works because I went to the product page on the website, and verified the White and Black stock levels there.
I then changed stock level of Product Part White to 17, and then Product Part Black to stock level of 23. The BoM updated the stock level in the Variable Product but only for Product Part White. It did not update the stock level for Product Part Black.
So I went to the Bill of Materials in Variable Product, and up/down the number of Black Parts in the recipe, which caused the "Save" button to highlight. Then I saved the Variable Product and the controlled stock was the correct number.
It seems that I had to manually force the BoM to look at the Child for the Variable Product.
Any thoughts? Thanks! Jim J.