I have a setup where I store Pam's HarvestCraft crops in drawers. I took out an item, asparagus (item 5208 harvestcraft:asparagusItem), and tried putting it in a drawer containing onions (5219, harvestcraft:onionItem). The onion count in Waila increased by one, and the asparagus disappeared. Doing it the other way around (onion on asparagus drawer) does the same. It works the same when you double rightclick on a drawer where the matching items fit.

I should mention that this mod works awesome for crop storage :)

Is this problem specific to harvestCraft crops?

I suspect the answer to the above is "yes".

Digging in, I think HarvestCraft is abusing the ore dictionary pretty badly. Pretty much every item in HarvestCraft is registered against a separate list entry that makes every veggie / seed / food / etc. equivalent to every other veggie / seed / food / etc. I'll have to blacklist these entries and hope that other mods do not treat the dictionary this badly.

This should now be fixed in 1.1.4 with the addition of an internal blacklist. Any future issues like this will need to be reported so I can add them.