I freaking hate working from powder in small dapped dishes. It drives me ape poop as there isnt a great amount of 'drawing' space as the mouth of the dappen dishes are pretty small. This means it is much easier to touch the sides of the container when picking up a bead. If the bead touches the container, it grabs to it dropping into the rest of your powder whhich can contaminate it.
Personally, I prefer to work out of 8/10 oz size containers (yes I decant larger sizes into the 8/10 oz sizes). You dont have to work from 8/10 oz size, but the size of the 8/10oz mouth is perfect for me.
As far as the yellowing, I would bet your brush that the latest batch of yellowing is due to starch in your brush and not that your powder is contaminated.
Hope this helps