Lion sleep (or hibernate) closes all applications
I think this is the feature of logging out after inactivity that can be set in System Preferences. This is in the General tab of the Security pane with the option of "Log out after ... minutes of inactivity".

An Apple page describing this feature is available here.

Additionally, this issue is described in another Stack Exchange question that I saw recently.

I'm only on my iPad so can't check this out at the moment but seems like it might be responsible.