I have exactly the same problem.. in native, I have used a LOT of time trading, and I know most prices and where to buy and sell by heart, but since i started Diplomacy it has been much much more difficult to profit from. I also tried disabling economic changes, but it doesn't seem to make a difference.
Some of the differences:
Note: My trading skill is at where it always is when i trade: 4.
Velvet: You can buy this cheap at Jelkala in native, now its as expensive as its selling price, so its not even worth touching anymore.
Oil: Could earlier be bought at various Rhodok and Swadian Towns, especially Suno, at ~300-350 and sold at ~430-450, but now the buying price is up to the selling price, same as velvet.
Spices: This one is not as bad, but the selling price has dropped by ~100 everywhere.
Iron: Selling price dropped by ~50.
Raw silk: Usually could be sold at Veluca and Jelkala for >700, now its down to <600.
Flax bundle: Previously bought at praven at ~95-110, sold at ~200-220, now its ~120-130 and ~170-180.
Linen: Previously bought at Sargoth for ~120-160 later sold for ~250-270. Now its ~220-240 and ~240-260.
The list goes on. The evidence is pretty clear that something is wrong.
It's too bad, because I love everything else about this mod, especially the fact the lords can be let back to their original faction.