Harvested items (wheat/reeds) disappearing upon pick up (also taking place of boots)

What I expected to happen was...:

I would harvest wheat/reeds and it would collect the wheat/seeds/reeds into my inventory

What actually happened was...:
Since the Vanilla SMP server I play on updated to 1.4.6 I have noticed when harvesting plants that they will not be gathered correctly. They appear to replace boots (go into the boots slot) and/or just not be picked up at all if you don't already have the wheat/seeds/reeds already in your inventory for them to stack with.

I also noticed it happened with items that are created from wheat/reeds (i.e. paper). It may be the case with other items as well but these are the only ones I've noticed.

Steps to Reproduce:
1. Harvest some wheat and/or reeds without having any already in your inventory.
2. The reeds/wheat will disappear and/or go into the boots slot (and your boots appear to be deleted).
3. This also occurs if you throw the items from your inventory and try to pick them up (if there is no other of its kind it can stack with).