According to this article on Hacker News, Apple’s new iOS 4.3 runs JavaScript slower when embedding it inside a UIWebView. The same issue affects HTML applications that are designed to be added to the iPhone’s or iPad’s home screen and launched from there in fullscreen mode.

Apparently this is caused by the new Nitro engine’s JIT compilation being enabled only when JavaScript is run in the standard Safari browser. This could be a security feature, because JIT compilation requires write access to executable code segments in RAM.

In any case, this is something to look out for, and hopefully something that Apple will fix in future iOS versions.