Hello wastelanders, once again I've come across something in Fallout 4 that may easily get overlooked. As some of you may know you can store your junk at the workshop. One thing I have noticed though is when crafting, it's using items in the workshop inventory. Except it will use items that have multiple components to it. So basically it might use a microscope for one component and toss the rest.
The best way to scrap everything is to drop everything and go into workshop mode and each scrap piece. I know it's a pain in the ass but you're wasting lots of items and parts if you don't.
Then again some of you may have figured this out already!