iOS 6 safari, setInterval doesn't get fired
iOS halts almost everything in response to user touch to guarantee it feels responsive. The setInterval issue is known, and there doesn't appear to be a workaround.
setInterval pauses in iphone/ipad (mobile Safari) during scrolling
EDIT
During the "freeze" the timer will not catch up once the user releases the screen. The missed events are not deferred, but lost entirely (a bug).
Found this (scary but amazing) workaround, and it's working for me in iOS 6.0:
https://gist.github.com/3755461