We made some fondue the other night, and instead of being a nice smooth dippable fondue texture, it came out grainy and lumpy.  What went wrong?  Here's the recipe that we used:   1 clove garlic 3/4 cup Dark Ale or Other Beer 1 cup Emmenthal Cheese, Shredded 1 1/2 cups Gruyere Cheese, Shredded 1/2 cup Appenzeller Cheese, Shredded 1 tbsp Corn Starch   Slice garlic in half, rub in fondue pot.  Warm beer without boiling.  Mix cornstarch and cheeses.  Stir cheese into beer, one handful at a time, allowing to melt in-between additions. 
I suspect that your cheese curdled.  This happens to me if I overheat the mixture- especially in the presence of acid. (I don't have any experience with using beer.) The cornstarch is there as a safety net to prevent this but obviously it is not infallible.  Turn down the heat and try adding a little more corn starch- it may not get back to perfect fondue but you may be able to pull it back to edible. 