I wouldn't really worry about it guys, there is nothing wrong with the file its just a PS display issue.
When viewed at 100%, (which you should always do regardless), you'll notice that there is no difference in the image...flattened or not.
The [flattened] version is in fact the correct output of the layers, what you are comparing it to is a compressed version at less than 100% zoom.
If you look closely at the image you'll see that at 3200% zoom you have detail only 1px x 1px. If you zoom OUT then there comes a point where to display a 1px square on your monitor just becomes impossible....so its not displayed at all.
This is the 'darker' version you 'think' is correct....but its not...its missing lots of detail purely because of the size of the detail....it simply cannot be displayed at that zoom level.
The 'flattened' version appears different because PS is NOT very accurate when it comes to mathematics. Adobe adopt a method called 'Quasi 15bit' for its calculations, (mathematically, not the menu option), and its not very good at best...this is used extensively throughout so when you 'flatten' your layers you get an image more representative of the truth....confusingly at the same zoom level.
Quite why this happens I don't know...but then who knows what happens in PS period! 
Its also this 'Quasi 15bit' method that makes the histogram pretty much useless, gradients from 0 to 255 impossible and no doubt a whole heap of other things just totally out of whack.
Your circumstances just happen to show these inaccuracies in a more dramatic and visual way to normal, but I can almost guarantee that they happen all the time.
Make it a habit to ALWAYS view your work at 100% before assuming the worse.
Regards.
MrToM.
