Yes, I am using Darnified UI 1.3.1. And I see now that you're exactly right in that that icon is related to that ui mod.
However, according to the mod, that icon is inserted in front of any generic message that doesn't have its own icon. So, it appears that there is some hidden or null length error message that is being caught by Oblivion, but not displayed on screen.
In any case, i uninstalled the UI mod, and I'm still having the same problem. (Just running Oblivion.esm and MountainTower.esp)
I don't know of any way to dump logs or error messages, although I did try to set debugging on(console:tdt). Didn't get much out of it, although typing "sdt 5" in the console returns some very spammy script related messages.
Poking at it some more, I found that if i disabled script processing (console: tscr), I could activate the retriever successfully and retrieve things I manually put into the jars, but activating the sorter still puts it into my inventory. (the hotfix keeps it as an activated item, but activating it still doesn't do anything.)
I really am feeling like I somehow messed up my base installation...
Ok, I have to admit that the UI mod was truly the last place where something could have gone wrong IMO if you're not loading any other mods. I can't think of anything else than actual save game/installation corruption now. If it's at all feasible, I suggest re-installing the game (do remember to back-up mod load orders etc).
As for the icon showing up, there's a block of script before the actual script that is designed to completely block out any messages about ingredients being
removed from OR
added to the inventory. It does this by overloading the message queue, so that while the spammy removed/added messages are still there, they are now invisible to the player. DarNified UI still shows that icon for those invisible scripts, therefore mostly defeating the purpose of the item spam blocking part of the script.
Basically you shouldn't see any messages for either the ingredient sorter nor the ingredient retriever, apart from the one screen that should pop-up when clicking on the ingredient retriever.
Edit: Before re-installing I'd suggest starting a new game with only MountainTower.esp loaded and using console commands to get the gold to buy the tower. Then test if there truly is something wrong with the base game installation and not just your save games.
Edit 2: Do you think the hotfix actually fixes the bug for anyone or should I just take it off the air? I mean, if it's not fixing anything for anyone...