This bug was fixed in the package pinentry - 0.8.0-1ubuntu1

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pinentry (0.8.0-1ubuntu1) natty; urgency=low

  [ Rohan Garg ]
  * Add kubuntu_01_fix_stayontop.diff to make pinetry-qt4 stay on top (LP: 
#657219)

  [ Scott Kitterman ]
  * Drop obsolete pinentry-qt package
    - Drop package from debian/control
    - pinentry-doc suggests pinentry-qt4 instead
    - Switch configure flag to --disable-pinentry-qt in debian/rules
 -- Scott Kitterman <[email protected]>   Sun, 17 Oct 2010 12:26:29 -0400

** Changed in: pinentry (Ubuntu)
       Status: Triaged => Fix Released

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pinentry-qt4 doesn't raise on top, need to select that window manually
https://bugs.launchpad.net/bugs/657219
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