At level 80, I skipped Cataclysm and went straight to Pandaria. Even as my warrior leveled up, and that heirloom axe increased in iLvl along with me, Dugi still ranked that iLvl 87 sword higher. I kept picking up new 2h weapons, and Dugi kept rejecting them in favor of that Wrath sword. That's when I noticed that all of these Pandaria weapon drops, even weapons 20 iLvls higher than the Wrath sword, had secondaries under 20. So even though Dugi Gear Advisor is showing that a new weapon would provide a DPS increase, it still prompts me to re-equip that Wrath sword every time I equip a new weapon. Meanwhile, I've kept the heirloom axe in my bags, assuming that at some point its stats would once again beat whatever I had equipped, but nope, it doesn't, according to Dugi.
I think this may have been a case of that specific sword simply having wildly inflated secondaries. If I recall correctly, when I played during Wrath, +STR and +Hit were the stat kings for plate DPS classes (I remember all the guides recommending +STR gems in every slot and +STR enchants on everything) and secondary stats were, well, secondary, and inflated secondaries on a weapon weren't that big a deal. But now that secondary stats have so much more importance, I suspect that an "outlier" weapon like that just wreaks havoc with modern calculations, so that all the addon sees is that this particular sword offers +15 more Haste and Crit than everything else that drops.
I dont know why i havent posted this earlier but i have been using Zygor for more then 2 years now and i simply love it! Worth every penny i paid for it. Speeds up leveling process and makes it pain free. And when your max level fun is not over and Zygor will help you every step of the way whether its Reputation grind, daily quests or achievements its brilliant.
I love this addon and the accompanying standalone tool.  Thanks so much.  In particular, I enjoy the commented section including bagged items so that I can easily simulate comparisons w/ the copy= command.  Is there any way to include bagged relics for comparison as well?  The addon must have access to the identifiers, and it would be MUCH easier than trying to match them on Wowhead.