I actually noticed this bug in 1.4.7, however I just tested in 1.5.2 and it's still there. It can be reproduced by putting a stack of dye and gunpowder in a crafting bench. Pull each star out one by one, and try stacking them in your inventory. Occasionally the stars will not stack, even though they are identical. Relogging seems to allow them to stack again, as does throwing them on the ground and picking them up again. Firework rockets show the same behaviour.
I checked the NBT data for 2 stacks that would not stack together, and the data is identical (included image)
Please add any additional information to MC-13565.