tl;dr Recently crafted potions aren't reliably stacking with ones previously crafted and stored, despite not having been an issue previously. Additionally, previously stored potions cost more to re-store, and can be sold to vendors.
More specifically: I had a number of potions crafted and stored previously, which I withdrew from the Drain to transfer to Port. At the same time, I crafted some additional potions to store alongside them (done countless times before, no issues with stacking). Now, the bank at Port is demanding 200gp to store the older potions, but 10gp for the ones crafted today (so it seems the system is assigning different values to the previously stored potions?). Additionally, while crafted potions generally cannot be sold to vendors, I now have the option to sell most of the previously crafted ones.