Comment 64 for bug 418242

I'm also having this problem on Ubuntu 13.10, Inkscape 0.48, and Netbeans 7.3.1.

The easiest workaround I have found is using Diodon to clear the clipboard after copying anything in Inkscape and before clicking on another affected application like Netbeans.

Just install Diodon
sudo apt-get install diodon
and it will add an icon to the panel (top right) where you can easily manage and clear your clipboard.

Really all you have to do to avoid the endless popups is add anything other than an Inkscape object to the clipboard, so with Diodon you could select a recent clip. I have noticed though, that if you have the Diodon automatic paste enabled and you have an inkscape object selected when you select a clip from Diodon it may change the object's settings like color and opacity.