Turtle Caramel Turns to sugar

I can't back this up with any evidence, but I think the reason it doesn't work well is that at the temperature required to caramelize sugar, the other "impurities" in brown sugar will be burned and gross. You might be able to get a similar effect by making regular white-sugar caramel and then mixing in molasses after it has begun to cool.

If the crystals have formed in the same way the crystals form in Honey, then you could try warming the caramel. Honey forms crystals over time, and these are removed by placing the honey in hot water for an hour (you will need to keep the water hot, above body temperature but not boiling).