i just reflashed cyanogenmod 11 and noticed the same bug with disappearing shotcuts on homescreen. it was complete empty after a reboot (only the icons near the menu button, there phone, text messaging, camera is on stock, are still there). this happens random and firstly widgets are gone and after ths the shortcuts after a other reboot. very strange, this even happend on m new fresh install. also some times my phone wont get past boot loader unlocked message, then i have to hardreset it. seems relly strange... any ideas
are you using/have been using/have some app for the purpose of storage swapping? eg. app2sd, link2sd...?
Have you tried without installing any apps?
Surely some app you have is causing this - I have never experienced it, and I haven't heard of anyone else having such problems...