Harvestcraft recipes that require dye (such as colored candles and colored food items) use the vanilla minecraft dye specifically instead of the ore dictionary entry for that color. This means that the blue, black, brown, and white dyes added by Pam's Weee! Flowers can't be used in those recipes (for example, weeeflowers:bluedyeitem can't be used to dye harvestcraft candles blue because the recipe requires minecraft:dye:4 instead of ore:dyeBlue).