I am currently having an issue on my private server (like 3 people) that for whatever reason items that would normally stack (same items won't stack together this issue also seems to affect crafting recipes as I find myself having to go into creative deleting items that I am using to craft (example being planks,cobble,iron,redstone) and creative spawning in same items and then crafting works. Now the main issue with crafting is mainly thaumcraft arcane table and even with research I can't use items I crafted to make node stabilizer until I traded my crafted items for the creative spawn ones.
Here are some pics of items in my chests that won't stack:
Take a look at the greatwood saplings they won't all stack.
Look at the gold ingots (all from vanilla minecraft) and copper ingots from IC2.
I have googled and searched but this issue is so odd only seen this on Purplementat's channel on his running red series with chicken (uncooked).
Another One Bites the Dust
Applied Energistics 2
And I tried with inv tweaks only client side and in server both had no benefit or negative effect.
I think you misunderstood me a bit the 2 unstackable piles of gold ingots are both vanilla gold ingots and copper is both from IC2 as well as the great wood saplings I have also had this issue with dirt and cobblestone and even torches not stacking together.