I've noticed and read about the difference between running an app in Safari and running it after saving it to the homescreen (even with iOS5).
I thought maybe it would be handy to have a list of known issues so some people can stop searching for reasons why the app is behaving differently.
Since i am not experienced, my contribution will be very limited
1. Speed: safari runs significantly faster.
2. Small hesitation after startupscreen: after loading, a screen with black and white squares, followed by a black screen (shortly) appears.
3. ...
It would be nice if some people could add a few, i can imagine there are other problems...