For some reason after researching the belt boxes all my recipe's seem to be requiring stacked items to craft.

https://imgur.com/a/vWkS6At this is what the inserter's are asking for. Not sure if another mod is causing the issue or if it's a setting I'm missing. I'm going to guess i did something to make it go wonky.

Probably Omnimatter. That mod is a menace.

I am using Omnimatter, so there's a good chance but I also have a bunch of other mods even a couple I made. For the life of me though I can't figure out what's causing it.

I had that exact issue, after some trial&error i came to the conclusion that this is caused by the omnilibrary mod. i've asked about this in the omnimatter discord, but no answers so far

The issue is that it seems to be treating the stacked items as raw materials