Yeah, I kind of figured that out after realizing it was doing it to everything I interacted with.
Yes, that part is working as it should. I started seeing some actual merchant numbers when I turned off the save-game reset.
Good

One thing I've noticed, there are a couple of merchants that were added by DLCs, the one in Wawnet Inn and the one in the Mystic Emporium. By default they both start with 2000 gold but EE starts out by reducing that, depending on what the tnoEE.max_gold is set for. Why is that?
Because I don't like merchants that are so much better than others without a good reason (the 8000 gold merchant added by B&M is the worst, AFAIK). But as you noticed, this too can be controlled in the ini, with the "tnoEE.max_gold" setting. This is 1.1 by default, which means that no merchant is allowed more than 1.1 times the standard merchant gold - where standard is dependent on its mercantile skill:
<= 30: 600
30-40: (Skill - 30) * 20 + 600
>40: (Skill - 40) * 10 + 800
So with default settings of 1.1, Aurelinwae at the Mystic Emporium; added by Wizard's Tower (Skill 6, Gold 2000), will not have 2000 gold, but get its base gold capped at 600 * 1.1 = 660 gold. Of course, those 660 will be multiplied by "base_multiplier" etc. I find such merchants with so much gold and low skill to be an immersive-breaking exploit, but have no problem with others liking to have some merchants with more gold - especially with dynamic barter gold. So you can increase "tnoEE.max_gold", or set it to 0, which means no max-check.
All in all I'm pleased with the way it's turning out, especially with Living Economy-Items thrown it.
Glad to hear that

I'd really like to see take a stab at a new version of that. You could probably do some interesting things now with all the additions in OBSE.
Yes, I have started to consider how to implement this. My idea is to have each merchant type (Smith, Alchemist, etc.) and each city have individual multipliers for each item type (Weapons, Potions, etc.) - which is much the same as LE-items has. But with instead of LE's hardcoded base values (which overrides repricing from other mods, and fails to work for any mod-added items), I plan to just traverse the player's inventory just when you activate a merchant, and then read each item's current gold value, store it in a temporary array and apply the multipliers. And when you end the trade, I traverse the temporary array and reset all gold values. I will probably do the same with the merchant's inventory and his merchant chest to affect the values the merchant offers as well.
This way, I will catch all items, included those added by other mods - except items stored other (than the merchant container) chests owned by the player. But I can probably catch those too by calling "GetFirstRef 23 0" to find all containers in the merchant's cell and do the repricing on all items found in those containers (if the container is also owned by the merchant). That should catch every single item the merchant offers, AFAIK.
I'm not sure if I start working on this, or on new functions for Map Marker Overhaul after Enhanced Economy 2.1 is released (which I assume will be out within this week), but I think I have the implementation pretty well laid out.