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According to the Register Apple is throttling web apps:

If a web app is run from the iOS 4.3 home screen – in other words, if it is saved to the screen alongside local apps downloaded from the Apple App Store – and launched into full-screen mode, it runs roughly two to two and a half times slower than it does in the browser, according to various tests. It appears that whereas Apple has updated the iOS 4.3 Safari browser with its high-speed Nitro JavaScript engine, Nitro is not used when web apps are launched from the home screen.

Is this true?

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It's more that Safari was being boosted in 4.3 and that that boost was not available to Web Apps on the homescreen

According to ArsTechnica this is fixed in iOS 5.

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