I was playing around with my gear a bit lately, and found a case where seemingly clear upgrades are not being included. If I lock them in manually, they show up as a big upgrade.
For example, if I lock in the ilvl 460 tier 2 Echoing Void bracers, and re-optimize, it shows a ~4% DPS upgrade, which seems pretty major, while I’m still at my toughness threshold too after the optimization. The same goes for the 445 tier 1 Twilight Devastation bracers I have too, to a smaller degree. There may be other cases too, haven’t looked through all my items yet.