You are right there is only one javascript thread in the render process. When
JS execution is paused we still need to process incoming commands to make
inspected page's UI responsive and to process DevTools' commands like
e.g. 'step over'. To make sure no JS is executed in the page while it is
paused we suspend all possible JS entry points including DOM event listeners
and timers. It looks as if CSS3 animation wasn't handled properly. I filed a bug
You can add yourself to the CC list to track its progress.
Thanks,
Yury