Update**
Problem appears to be moving from top of chest to adjacent items .125 higher that have a block 2 squares above (to simulate a roof)
I tested going from top of chest to (dirt, crafting table, furnace) and was unable to move to that space if it had a block 2 squares above it.
Place a crafting table and chest in the ground (even with the surrounding ground.)
Place a roof (I used dirt) two blocks above the crafting table.
Now unable to move from chest to crafting table.
Height difference of blocks preventing movement to crafting table?
Able to move from different blocks of exact height (from dirt to crafting).
Able to move from crafting table to chest without issue.
This is a feature which has existed for awhile and allowed for the creation of one-way doors. (See http://minecraft.gamepedia.com/Soul_Sand#One-way_and_Minecart-only_gates) for more info.)
It's possible that it was originally a bug, but it's been around so long and allowed for so many creations that I very much doubt it will (or should) be changed.