Haven't tested with backpacks/anything else but:
Collecting Lava in Buckets bc I alr have the rest of my backpack slots filled
Tried putting them in Shulker without placing shulker
had 43, now only have 27, maxed out at the storage of a normal shulker.
Sophisticated Storage 1.21.1 NeoForge

I can try and recreate it in a testing world in a bit

yeah thats weird, testing again, its not happening again. maybe I just actually dropped that many buckets in the lava on accident who knows. anyway closing bc im not even sure if it was a bug anymore

Have you perhaps got Quark in the modpack with its stashing to shulker boxes enabled for sophisticated ones as well. That would do exactly this because it treats sophisticated shulkers as regular ones and stores the data where vanilla would expect it.

Actually Quark doesn't seem to be released for 1.21 yet, but I just tested and I am unable to recreate so I will need steps I can use to recreate and for you to make sure this is happening with just Sophisticated Storage alone or provide a the minimum set of mods with which it happens.