I know when you are painting the outside you need to wipe them down with rubbing alcohol. Perhaps you could try rinsing out the inside with rubbing alcohol and allow to dry.
If it is in your budget, get paint made for glass like Gallery Glass. If not, there is an additive that can be purchased from Decoart I believe that is mixed with regular craft paint to work on glass. Also if you just want to paint the balls all over, the easiest way is to remover the cap with loop from the top and pour paint INSIDE the balls, swirl it around inside for a few seconds, then turn it upside down in a styro or paper cup and let the paint drain out. It can be reused. You can do this with a couple of colors and you get a really nice marble effect.
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