Easy recreation on my end. (Modpack ATM3 v5.4)
Shift-clicking an itemstack from your inventory into iron,gold, or diamond storage crates will fill the current stack in the crate and null the rest of the items.

MC version 1.12.2
Forge 14.23.1.2562

This also seems to happen when shift-clicking items out of a Quantum Storage Unit, if there is a partial stack of the item it will take 64 from the QSU but only fill that partial stack.

@modmuss50 did you break the shift click code in RC again?

Uhh, I could have done. You use RebornContianer right?

yup

For those wondering, the recent release of RebornCore (3.6.1.183) has been tested and does not fix this issue.
EDIT: Also 3.6.2.187, 3.6.4.194...
EDIT2: Fixed in latest compiled RebornCore. Thanks CursedFlames!

I have been away for the last 10 days so I have not been able to look into this

Haven't tested it, but it looks like this issue might be caused by this line in the shiftItemStack method. The itemstack count seems to be set to a negative, which presumably empties the itemstack.

This should be fixed with the next RebornCore update.

Yup