When I import from the add-on I find that Auto Gem / Enchant gives me a different result to suggestions in Best In Bags with an unchanged set of gear. Which should I use?
Are you looking at your highest priority spec? Best in Bag may be selecting different gems/enchants due to shared pieces with other specs that are higher priority.
Yes - I only play one spec (WW Monk). It is set to be my highest priority - the others have never been activated. The only difference on that gear was one enchanting recommendation which said Mastery in one place and Haste in another. I have since upgraded the piece in question (neck) and now they both say the same!
Even if you don’t use MW & BM, you still need to configure their gemming, enchant & gear sources in the filter sections (the button that looks like a funnel); this could be skewing the results you’re seeing - if anything, I’d be inclined to set these options to absolute minimums to give your WW options the absolute best priorities.
Try this & ‘report back’ - if it’s still a problem, then post an export string to see where there could be issues.