All Flightstones/Crests upgrades show the same value, no matter what stats are on them or what trinket effect they have. And even if an item shows as an upgrade, after upgrading it Best in Bags doesn’t use it. for example this shadow orb that was shown as a 0.25% upgrade in Upgrade Finder shows as -6.31% in BiB:
Snapshot: f55baa66013342c087b8e9499b176ced
Thanks for the bug report, that’s really weird!
If I increase the allowed upgrade level to e.g. 593, then the ranking looks correct.
I’ll take a closer look today and figure out what is going on with this ranking at lower upgrade levels.
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We just posted an update that should fix this issue. Refresh the page and give it another try.
Also as a side note, we put in an estimate for Shadowed Essence – it was one of the few trinkets without one because I had no idea what it would do. It’s still a bit tough to estimate because I’m not sure how often the pet casts its damage spell.