Removed icon folder from Launchpad keeps coming back

After installning Yosemite the launchpad all icons on the Launchpad were shuffled around and when I organized them and reboot the system they were back in disorder. So I found a solution online to remove the .db in the library and that solved the problem.

The issue now is that every time I reboot the system two empty icon folders (that I keep removing) keeps coming back.

Is there any way I can get rid of them permanently and keep Launchpad remembering all my settings?