Your description is REMARKABLY similar to the MANY descriptions I've read (incorrectly attributed to mods other than the real culprits).

I would put MAI real low on the list of culprits were I you and instead I would focus on mods that alter storage and mods that alter hauling behavior, or behavior in general. For example Pick Up and Haul combined with LWM's Deep Storage, in the wrong order, will do what you are describing. Extended Storage too. Also mixing storage mods can cause this (as in even having more than one installed).

I've also seen this behavior with crafting where I have multiple workbenches/colonists pulling from a single Infinite Storage (family) building while Common Sense mod's haul items to workbench is enabled (AWESOME feature btw). Actually the Infinite Storage family of mods have had a bunch of issues with multiple pawns crafting from same source (most have been fixed though I did still have pawns using 70+ meat when they needed 7).

I've also read about stuff like this with Quantum Storage, IMO that mod hasn't gotten back on it's feet post 1.0.

I've also seen this in mods which 'borrow' some older Combat Extended code now running on a newer version of Rimworld than the code was originally written for - usually shows up around food, for no obvious reason.

Solving the issue will likely involve a lot of reading to find which mods might have issues and trying different load orders. Often behavior mods AFTER storage mods clear things up though that's not always the case.

Good luck.

The Darkness truly is Profound!
I am going to try swapping the order of deep storage and 'pick up and haul' and see how that works. Thanks for answering a question before I even asked it :D