Thank you very much for your post.
I've tried to reproduce the issue on my end but it's working fine for me. Please, make sure that ATUM and Product Levels are updated to the latest version.
Note that when you change the purchase price of BOM components you will need to re-load the page of the parent product to see the changes.
If both plugins are updated and the system doesn't update the purchase price when reloading the page, please open a private ticket here and leave us admin credentials to take a look into your site (Add a link back to this post in the ticket description).