Why does Launchpad not remember my icon settings?
There is an Apple Discussion here that describes the same problem, and refers to this OSX Dialy link on how to correctly refresh LaunchPad, and fix a corrupted LaunchPad.

The short version of the answer is:


  Basically I used terminal to kill the dock with the command "killall Dock"
  
  Then I had to delete the dock database file located in "Home Folder/Library/Application Support/Dock" you get to your Library folder by holding down the option key while clicking "Go" in Finder.
  
  Then kill the dock again with the terminal command "killall Dock". 
  
  Finally After putting all my apps back where I wanted them they are now saving.