Using create contraptions to input into "limited barrels" clogs the storage despite having space for items to flow into. happening with both create chutes and minecraft hoppers, does not seem to happen on single player and unloading chunks on a server seems to make it happen more frequently.

Example

This seems to me like there's a mod in the pack that attaches data to stacks and clears the data once you pick up the stack into your hand - one mod I am aware of doing this is Origins so if you have that in your pack that's likely the culprit. Also it would be very odd if this issue was only happening on servers, there's no code in how items are transferred that's server specific, that potentially tells me there's some server plugin that may be attaching data to stacks, but hard to tell without knowing more about the pack.
I would definitely need to know what version this is both of sophisticated mods and create to at least try to recreate the issue.

Mod versions are as follows:

sophisticatedcore-1.20.1-1.2.69.1005
sophisticatedstorage-1.20.1-1.3.49.1167
create-1.20.1-6.0.5

Other related addons

sophisticatedstoragecreateintegration-1.20.1-0.1.12.36

We do also have origins in the modpack, and the issue hasn't been documented on single player worlds by any of the players

Alright in that case I can tell you that origins or one of its dependencies is the cause, if you remove those mods this issue should be resolved.

closing given that this is issue on Origins side