You've run into one of the most common browser scripting issue with animated webpages.
The reason why your application slows down is because the browser is a single-threaded environment. As soon as you forget that you'll get into trouble.
setInterval makes you believe that your actions will happen in parallel like in a multi-threaded environment. But what really happens is that setInterval pushes the action to the UI stack to be handled at a later time. But if too many things are getting in to this stack at one time some actions will lag. The setInterval will keep pushing new actions, but the old ones will be still there, and the whole rendering becomes a sluggish mess.
As to when it happens, it depends on the hardware/software capabilities. iPad has much lower horse power than a desktop PC, that is pretty obvious.
Things you can do in order to avoid lag.
Trade smoothness for speed: raise your delay between intervals, so as to avoid cumulative actions in the UI stack.
setTimeout: this alternative is very similar to setInterval, except that it doesn't ensures a given interval between repetition, rather focuses on how long the browser should wait until repeating the action. So in order to make it more like setInterval you may need to keep track of the elapsed time between actions and calculate the measure of the change that has to be taken care of.
Group animations: you can have one interval for some related animations (you manage a mini-queue for them) and so you decrease the actual setInterval calls, and gain more power over controlling race conditions.
Also make sure to read this piece of article:
Making an iPad HTML5 App & making it really fast (Thomas Fuchs the creator of script.aculo.us)