You need to use the "Wait" command when you see your crystal is unstable.
Actually from what I noticed, the "wait" command changes the color of the orb which somehow has a direct correlation to the success of your next synthesis choice - meaning, with me personally, when i see the orb turn white I hit Rapid Synthesis because I *think* white gives me a higher success rate and well Rapid Synthesis results in the highest amount of progress of the 3 choices, so if I succeed I am boosted up well. Now, when a "crystal" goes haywire on me, I allow the time to drain out and it seems to do something...this doesn't change the orb color but something is altered with the crystal. Still trying to find common trends with crafting but overall I'm finding it interesting...if it wasn't for the **** UI lag, take me an hour to put my recipe together! :S.
Can't believe this game is almost at release, I can't wait any longer! :D