Well, I never have icons kicked out of Fences unless its MS Office documents Icons, which is known issue, or there is update done on that particular Program which make it install a newer version hence it move to desktop. Fences Desktop pages itself, I don't see it making it move icons out.
But back to your original issue, yes, it is "not easy" to properly align those fences for me too. I have forward your problem/question to Stardock Support Team for their assistance. Please keep an eye on this thread for any updates. We appreciate your feedback and patience.
Basj,
Stardock Community Assistant