Rather self-explanatory, some items don't stack to the 2 billion limit as it's said in the tooltip.
Not sure if this is something that can be fixed due to how Minecraft handles stack sizes internally (I've not been modding for a while so I wouldn't know)

If this is intentional then that's fine, was just weird seeing Ender Pearls "only" stack to 500 million (and items that don't stack by default to "only" 33 million)

Oh also, this is on All The Mods 10: To The Sky version 1.1.2 which has Sophisticated Storage 1.4.49, Core 1.3.64 and Backpacks 3.24.21

Ok, so this one was a bit confusing to be honest because what the Omega stack upgrade actually raises is the stack multiplier to maximum which is based on the max int divided by 64 - x33,554,431. I have just updated tooltips of Omega upgrades (both in Storage and in Backpacks) in the latest releases.