Yes I have the same problem. Dual monitors. Whenever the machine goes to sleep, upon wakeup, everything is moved around - EVERY time.
At best, some shortcuts outside of Fences wander to the other screen.
At worst, the screens get swapped over, and icons outside of Fences get shuffled around. That's a PAINFUL manual repair sometimes.
Sometimes a restore snapshot fixes it but not always. So we are getting to the point where the PAIN and WASTED time of having to repair makes one wonder whether FENCES is worth it.
One partial solution is to have all icons in FENCES.... then only fences get shuffled around and that means fewer items to relocate. But thats not a solution to benefit that becomes and annoyance.