I found a fix, that worked on Xubuntu and on Ubuntu 12.04. (cf.
http://doc.ubuntu-fr.org/jpilot?&#ca_ne_marche_pas)

Below are the steps, in French (cf. http://doc.ubuntu-
fr.org/jpilot?&#ca_ne_marche_pas) and in English

1°) installer les paquets syncbbdb, pilot-link, et pilot-manager 
2°) vérifier que vous faisiez partie du groupe "dialout" (ou modifié ce groupe 
pour vous y inclure)
3°) redémarrer votre ordinateur

1°) install packages syncbbdb, pilot-link, and pilot-manager 
2°) check that you belong to the group "dialout" (if not, modify that group in 
order to belong to it)
3°) restart your computer

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https://bugs.launchpad.net/bugs/882054

Title:
  JPilot no longer connecting to Palm on port usb: under Ubuntu 11.1o

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