Is there a solution to this?

I once ticked the "Automatically remember running
applications" , under
System >> Preferences >> Startup Applications> >Options tab

Then after "unticking" this option, applications still starts up.
So I googled for a solution, which reads "Actually, sometimes the fix for this
is to make sure that
"Automatically remember running applications. .." IS ticked and there
are no applications running when you log out. Then, after you log in,
untick the box."

Which I did, but some changes I make to my system still don't stick upon
reboot.
Is there a permanent fix to this or Is there a cache or something to delete?