Comment 44 for bug 418242

I've also noticed a similar behavior (and I'm using Xfce 4.8 too -- I tried with and without clipman plugin activated, and this doesn't change anything).
In my case I didn't loose the control over Inskcape because the GUI was still responding to keyboard actions. And after few workspace shifts and clics everywhere it was working again. But it seems to be a side effect to the other problem, because if the warning windows don't show up, I don't have any problem.

And those warnings actually come from the Gimp and JessyInk extensions.
If you don't use them you can remove/deactivate them and you'll get rid of this annoying Copy/Paste behavior.
I've only commented the line that raises the warning in both Python scripts (gimp_xcf.py and jessyInk_export.py) so that I can still use them. Now copy/paste works like a charm for me.

But this NOT a solution to the real problem, because I think the extensions are doing the right stuff. The real problem seems related to the crazy way Inkscape is managing his internal clipboard. Unfortunately I don't have time to investigate more. I was trying to figure out why Inkscape uses Gimp or jessyInk extension during a copy/paste operation, so I just took a look at the src/ui/clipboard.cpp file and saw that they are doing different things using the available extensions -- but I didn't go further because I don't have time (and skill) to do it.
Maybe this is a good place to start or perhaps I'm wrong, I don't know. But I hope this can help.