It seems as if the latest update of Quark causes Cooking for Blockheads' storage containers (Kitchen Counters and Fridges in this case) from working with Merge/Deposit from Quark.

I've tested the Merge/Deposit with three separate storage mods and they all worked, so it seems something specific with Cooking for Blockheads.

Here's what I'm running:
MC 1.12, Forge 2589
Cooking for Blockheads 1.12-6.3.16
Quark r1.4-121

I've made a bug report for Cooking for Blockheads at TwelveIterationMods/CookingForBlockheads#255.