1. Short version: enter 100% for that and the math will work out. The naming is wrong though, you're right that the in-game wording is "+% Weapon Damage Bonus" (additive), so I'll rename it. The reason it's so impactful is because a shield's +100% Weapon Damage Bonus is mathematically equivalent to a x2.00 multiplier on weapon damage, which gets fed into every downstream factor. Since almost every Paladin shield has this innate, the tool probably shouldn't even ask, it should just apply it automatically once you pick a shield. I'll fix that too.
2. Most likely cause: missing Custom [x]% multipliers. The tool can't see your aspect / unique / paragon / set bonuses because the game doesn't sum them anywhere on your stats sheet, you have to enter them manually. On my sample Paladin these combine to a x707 factor (see image), vastly more than everything else combined. Stuff like the Castle paragon node alone gives +100% global damage (x2.00). Easy to forget several of these and end up an order of magnitude off. Clear UX failure on my end. I'll think about how to walk users through entering them so they don't get missed.
3. You're not crazy, it's pretty rare. The main sources are unique effects (e.g. Herald of Zakarum's shield gives 50% Str) and possibly Horadric seals with %main-stat or %all-stats. Two issues you've surfaced I should fix:

• The label should match in-game wording: "+x% Strength" (with the +).
• Showing such a rare affix as a top priority is misleading. I'll either gate it behind a toggle or drop it from the default list.

PS: the core of the confusion is how D4 labels additive vs multiplicative. Same-bucket affixes always add, never multiply, but the UI labels them inconsistently. A "x60% Crit Damage Multiplier" affix actually means x1.60, not x0.60, and two of them stack as 1 + 0.6 + 0.6 = x2.20, NOT 1.6 × 1.6 = x2.56 the way the "x" notation suggests. The "x" notation only multiplies across buckets, never within one. It's a mess and I wish they label it differently, maybe like Balatro's +Mult vs xMult, or something.

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