Replanter upgrades dont seem to work with modded plants from Pam's Harvestcraft or thermal series plants, they just get broken anyway.

Fixed in 5e55839

As of today, my replanter rats will harvest Pam's Harvestcraft plants and other mods, but will not properly deposit them into chests. They hold the items in their mouths at the chest, but will not deposit like they do with vanilla crops.
Case in question involves the replanter upgrade alone and attempting to deposit into a vanilla spruce chest.