I have had this issue also, in this and other past versions. There are so many quick workarounds and ways to do things i usually don't dwell on it, just get the task done and move on. So it's hard for me to remember where and when.
The "Copy, Paste, Delete Hole" thingys will go a little wonky on me when I'm working long sessions. Sometimes if I clear out the Pic Cashe folder it clears that issue up. Sometimes that will just fix it temporarily. I'm guessing that sometimes it is some kind of buffer issue.
Good Luck.