At the least there could be a loose bottom bracket cup/thread. They sometimes work loose or corrode. When there is corrosion on the threads it can make the threads creak/pop. To remedy this, remove it, clean it and grease the threads.
The other possibility is the arms/BB interface.
Even the cheapest OEM ISIS drive crank will last without creaking if it is maintained. I am willing to venture that you did not check your crankarm bolts before the creaking started. The arms will set in place normally, but some units will work themselves loose. This means the bolts should be loosened and retorqued at least monthly, if not more often. It is a risk otherwise, since when the creaking occurs it means there is a sizeable ammount of movement. That movement means wear on the interface is happening and can prevent the arm from bedding in the future.