I've played around with it for most of the morning, processing last night and this mornings avi's.
It took a while to figure out where things were hidden, for example, the stackgraph, where you move the sliders to determine how many frames to stack.. That was hidden for a while and it kept stacking ALL the frames including the bad ones.
It's much much faster than the old version, and has some cool new features, some which I have no idea what they do just yet

I don't think i'll be going back to version 2 now.
Seeker as for your problem, I had that once or twice, but closed it down, re-opened and then it was fine.