If anyone on Windows 10 is still having issues with the item pick-up/inventory bug, I may have found a solution.
I've found out that I never get the pick-up/inventory bug when I'm running screen recording software. I'm using Shadowplay from NVIDIA and I've completed the game without an issue. I've also tried the free Apowersoft recorder that you always have to access via their website. It's not good for recording gameplay, but if you want to play Infernal Machine then it's still a useful alternative if you don't have a built-in recorder like Shadowplay. So yes, that means that every time I want to play Infernal Machine, I have to record. Every. Time. Oh well. It's sooooo much better than constantly resetting the level or using strategic quick-saves every time I want to pick up something.
Apparently, if I read this correctly, running Windows Media Player fixed this issue in Windows XP. Just for kicks, I did try this, but it no longer works. Recording software seems to have taken Media Player's place as the go-to fix.
As a disclaimer, I cannot promise this will work for you as I have only tested this on my computer. I don't know if it has something to do with my current set-up or whatever. But I think it's worth checking out.