At least twice so far, only during quests, I've had a problem picking up items from chests. It happened on the Beware the Purring Liar and the Thick as Thieves quests (I think there was another one, but cannot remember).
After the chest is unlocked I could not use R to take everything, I had to double click on the item description to pick them up. In the Thick as Thieves quest, I got a bounty trying to use the R key, because it also took me out of stealth (my char stood up, IIRC).
Outside of quests, I had no problem using the R key.
The other small bug is that many of the silver locked chests found in houses and businesses in Elsweyr only have gold in them. Those were not chests that had been opened by other players. I had to pick the lock in each one of them and they only had gold coins inside. As far as I'm aware, all locked silver chests contain some gold and at least one "treasure" item in them.