Jonathan,
After playing a bit with the openbox conf file, I think this one should be 
sufficient :

    <application name="lxpanel"
                 type="dialog">
      <focus>yes</focus>
    </application>

Could you try with this one, and tell me if you see any regression ?
Thanks.

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https://bugs.launchpad.net/bugs/889414

Title:
  Run dialog opens up in the background

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