this is strange indeed - when I leave enable at launch ON, and the backgrounding method is native, everything ends up being backgrounded somehow (and if you leave badge ON in backgrounder, it's easy to see)... this will kill the memory in no time...
I'll think I'll stick to the override method for now.
Yeah I tried with non iOS4 apps (Amex and Citi) both just fully closed when I press home button and I checked in SBSettings processes
Whereas iOS4 apps such as Reeder, Skype, and others all suspend to RAM when home button is pressed. They are on processes from SBSettings and they indeed open from where I last left off.
EDIT:
It seems that There is indeed something fishy going on. As I mentioned before, I tried non iOS4 apps (Amex and Citi), both did NOT run when I close it. However, when I tried Meebo which is also not updated for iOS4, it runs on the background with blue icon!
EDIT 2:
I tried to follow RedCloud75013 method and disable enable at launch option and create exception ONLY for Skype. Yes Skype works and Meebo doesn't run anymore. However, WunderRadio ceased to run on the background either!!!! Pandora stopped running on backgorund too as well as Reeder and every single other app!!!!.
Uninstalled Backgrounder, Skype doesn't work (of course) but everything else works fine and no crazy apps running on background when they should only be giving me push notification instead of draining my battery.
I tried fast app switching on Reeder, Bloomberg, and Kindle -> all works and it returns me to my last place.
Meebo also gave me Push notification... so it works ok.
For now, I will just uninstall Backgrounder and say screw you Skype.
Hypothesis:
Seems that when you install Backgrounder, it kinda "takes over" the background API handling.... And causing this problem where it's running apps that should not be running (eg: Meebo should only give you push notification and not actually running on background)