I have the same problem. At my office we used to have the screens set to black to help ease the transition for new folks from AutoCAD to ArchiCAD. But then this copy-paste thing between stories (and also between multiple instances of AC) came up. So now we set our screens to dark grey. Nevertheless, even a white screen still has its elements turn black. Still waiting on a hotfix for this obvious and annoying bug.
If you haven't found the workaround yet, here's a link to another thread on this same problem:
http://archicad-talk.graphisoft.com/viewtopic.php?t=18428&highlight=copy+paste+black
What I've found to work even faster, because my "Automatic Pen Color Visibility" thing is always toggled ON, so that thread's solution might not work for you, is to do a rebuild: on Windows, it's CTRL+Shift+R. So far, across all 6 of our computers with AC11, the graphics card hasn't been the source, as they're all different and all of the computers have the problem.
And if even that
won't work, instead of restarting AC, go to a different story or a section and then go back to the story you wanted. That generally triggers a somehow more serious rebuild than simply doing it manually.
But the hotfix is coming...hopefully.
good luck
Zolli