So we found an issue in another plugin, and after further testing realized this was a Spigot/CB issue.

The player interact event is fired when you drop an item, whilst not looking at a block (ie: looking up at the sky)
If you are focused on a block (where you can see the block's hitbox) the interact event will not fire.

Simple code for testing:

@EventHandler
private void onClick(PlayerInteractEvent event) {
    Bukkit.broadcastMessage("Player interacted");
}

@EventHandler
private void onDrop(PlayerDropItemEvent event) {
    Bukkit.broadcastMessage("Player dropped");
}

Tested this on CraftBukkit and Spigot

Focused on a block, dropping an item:

Looking up at the sky dropping an item:

Included a little tester plugin.