When mining for example uranium, the unifying isnt stacking just in one stack, its divided into 2 ore sometimes 3 different stacks, even though the uranium from different mods is unified to immersive engineerings uranium. Also just regular mined stone is divided into different stacks and wont just stack in 1 stack up to 64 blocks. There probably are more blocks that behave this way, but this is what i have seen from testing.

And I cant add the different stacks onto each other, even though i throw the "same" blocks on the ground and them pick them up. Any ideas what causes this?

sounds like you've different NBT added to your items, by another mod

Also copper, tin and lead does the same thing.

are you sure that this is caused by my mod?
instant unify doesn't affect cobblestone (unless you added it to the config).
show your config file

edit: do you use unidict?

Its pretty hard to determine if this issue is caused by this mod, because if i try without it, all the ores drops as intended from respective mod. I havnt configured this mod, nor unidict, which im using too. I just figured this might be the place to start since it changes the block output from all ores into 1.

Reinstalled this mod and for the moment things seem to work as intended with unifying ores. Not sure why it behaved the way it did. I will do further testing

Edit: Problem still remains. It just all of a sudden switches onto a new stack with the recent one stopping at like 13 or 5 or low numbers like that.

Edit 2: I can confirm that even torches doesn't stack in on stack either. This is the only thing relevant in the game log: "Received passengers for unknown entity". This pops up now and then and kinda matches in time when a new stack is started.

Edit 3: After some time goes, i suddenly can inventory sort which makes every item go together in one stack slot.. This is really confusing.