I made a cell and placed a lot of custom chests in it. I each chest is a new base and each have a modified version of http://cs.elderscrolls.com/constwiki/index.php/User:Candlemaster/Item_Sorter to take things from my inventory and store them in different chests. This much works.

The problem is that when I take them back out of the chest, they are not in the chest nor are they in my inventory.

I followed the instructions in http://savageartistry.darkbb.com/tes-iv-oblivion-technical-info-f11/creating-a-chest-and-adding-items-tutorial-t130.htm (excluding the part where stuff is added -- All chests start out empty).
Each Chest is:

• is a new base object
  
• is owned by player
  
• is non-respawning
  
• is a persistent reference

What am I doing wrong?

A lot will depend on how you modified the Item Sorting script. It would be very easy to mistakenly have that grab back the item you just took out and re-sort and lose it for you. Post your version (in spoiler tags) so everyone can laugh look at it.

scn DB425SortChestHeavyBoots;original source: http://cs.elderscrolls.com/constwiki/index.php/User:Candlemaster/Item_Sorterlong Quantityshort Buttonshort CheckOnceshort atypeshort eqslotref pInvObjBegin OnActivate	if ( GetActionRef == Player )		MessageBox "[ Heavy Boots ]" "Deposit Heavy Boots" "Open Heavy Boots Chest" "Nevermind"		set CheckOnce to 0	else		Activate	endifEndBegin GameMode	set Button to GetButtonPressed	if ( Button == -1 )		Return	elseif ( Button == 0 ) ;Search Inventor		if ( CheckOnce == 0 ) ;Only go through the player's inventory once			PrintToConsole "Begun the search for Armor"			array_var each			ForEach each <- player.GetItems 20	; 20 = Armor				PrintToConsole "Found an Armor"				let pInvObj := each["Value"]				if eval !(IsQuestItem pInvObj)					let atype := (GetArmorType pInvObj)					if eval (atype == 1) ; Armor is Heavy						let eqslot := (GetEquipmentSlot pInvObj)						if eval (eqslot == 5) ; Armor is Boots							let Quantity := player.GetItemCount pInvObj							player.RemoveItemNS pInvObj Quantity							AddItemNS pInvObj Quantity							PrintToConsole "Heavy Boots Moved"						endif					endif				endif			Loop			PrintToConsole "LoopEnd"		endif		set CheckOnce to 1	elseif ( Button == 1 ) ;Open Container		Activate	elseif ( Button == 2 ) ;Exit		return	endifEnd

Seems this is not the issue. I used the http://cs.elderscrolls.com/constwiki/index.php/User:Candlemaster/Item_Sorter (Second Attempt - what all of these scripts work from) for a new chest with the following differences to the original code:

• new script name
  
• message box text
  
• if ( HVHGTOBSE.HasObse ) and respective else, comment and endif, as well as adjusting the tab depth of the code between

And yet the same problem occurs.

Not sure what is causing this. I have been testing this like mad. If I take all ingredients, they show up in my inventory. I tried taking 1, 2, and 3 times and they don't show in my inventory. But if I use the message box option for removing ingredients from my inventory (I will call this the sort option for now on) they show up in the chest again. I will continue testing. In the mean time I hope that someone might have a clue of what is happening here.

It seems the issue is the use of http://www.tesnexus.com/downloads/file.php?id=5118, though not the mod itself. I think it has to do with the fact that I am carrying lots of items (over 3K weight), while removing these items from the chest. Testing it with a lot less items in my inventory doesn't seem to have this affect.

I don't think the items are gone, for a couple of reasons. I can "sort" them back into the chest. I just think that there is an issue with seeing them in my inventory. A friend of mine who is also using the aforementioned mod also noticed something similar, he was disarmed, he picked up his weapon and couldn't see it in his inventory at first. It was later that he was able to see it again.

If I notice any thing to the contrary of this theory then I will post it here. In the mean time, I welcome anyone else to share in ideas they may have.