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.

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You received this bug notification because you are a member of Desktop
Packages, which is subscribed to inkscape in Ubuntu.
https://bugs.launchpad.net/bugs/418242

Title:
  Incorrect call to output plugins (with persistent error message) on
  copy

Status in Inkscape: A Vector Drawing Tool:
  Triaged
Status in “inkscape” package in Ubuntu:
  Confirmed
Status in “inkscape” package in Debian:
  Confirmed
Status in Gentoo Linux:
  Unknown

Bug description:
  UPDATE: After further investigation it turned out to be a problem related to 
the copy operation, in combination with a totally unrelated running Java 
program (FreeRapid).
  Reading some followups and other bug reports, it seems to be caused by the 
new clipboard management system (introduced as a fix for the bug #170185), as 
reported in bug #421597

  So far these applications are known to randomly trigger an input/output 
extension (on linux):
  - FreeRapid Downloader
  - jDownloader
  - xfce4-clipman-plugin 1.1.3
  - Netbeans
  - xfce4-settings-helper (Xfce 4.8)

  -----

  The original report was this:
  I'm getting this error when I try to edit a text object created previously 
with a font that's not available in this system.
  It looks like Inkscape has problems to resolve the font substitution and 
displays the error message in a popup window that keeps appearing again and 
again, leaving no other remedy than closing inkscape and reopening it.

  The error message is attached.

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