I don't believe there's any way to make dynamic clothing loop. This is one of the biggest problems with using it for units. I just resorted to editing the storyboards manually after rendering to try to smooth the jump.
I had the same problem with the simulation stopping too soon. It seems that the more complex the simulation, the more likely it is to do this. Try reducing the Drape Frames number: this seems to help.
One thing I've found is sometimes it's easier to use the Cloth Room to create a prop and then turn that into a poseable figure in the Setup Room - and then use that rather than try to incorporate a cloth simulation directly in the unit itself. For example, the large cloth collar that my Ethiopian Spearman wears, and the cloth draped over the left arm of my Abyssinian Spearman, are conforming figures that I made in this way. You couldn't do it for (say) a cloak but sometimes it can work quite well. The advantage of this method is that although it's a pain making the figure it's infinitely easier to animate - no inexplicable glitches, and it will loop.