Just had it happen again. This time, the canvas was very low res and misaligned so that the center of the game was in the bottom right corner. I pressed refresh and now the game is both misaligned and rendering upside down. Not rotated, flipped vertically.
I tried it in ie, and it said a problem with the page caused it to close the tab and reopen it. It did however work correctly after that, and didn't have the same problem when I tried it again.
Firefox, aside from a lousy framerate and taking so long to start the game it says the script may be busy or stopped responding, worked fine as well.
I then tried opening a new chrome window, and loading the preview again without repreviewing in c2, and it worked fine again.
It's seeming like it really is just a chrome problem - which I would be both happy and upset about, as chrome is what node webkit uses. I guess all we can do is just wait and hope that google fixes it, since there doesn't seem to be any way to reliably reproduce it...
Sorry about the incorrect c2 bug report.