After some experimenting it looks to me like this behavior only happens in the “CoronaViewer” folder in Dropbox. Simulator relaunches just fine on saved changes in other folders but with the Apps/CoronaViewer folder things seem to go weird.
I don’t know if that sheds any light on the situation but a fix would be helpful since frequently I’m trying out changes where I’m viewing both my iPhone and a simulated android phone.