Instead of using Epoxy to fill the buttons have you thought of using that colourless casting resin (I think it's Polyester). I must admit though, that that stuff does smell a bit whereas Epoxy is pretty much odourless. I was just thinking that the casting resin might not suffer with trapped air bubbles quite so much. You could probably dye it too.

edit: On second thoughts, instead of colouring the resin you could print out some small coloured filters to fit inside the buttons. You could use a similar method to my printed screens idea. This would be similar to someone elses (I can't remember who now) suggestion to put small transparent coloured pieces of plastic between the LED & the button to give various colours.