Inconsistent behaviour of applications and Launcher

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http://askubuntu.com – This is a question that involves multiple issues involved in creating a menu tied to a Launcher icon. I'm using a fresh install of 12.04 (AMD64 version). I've written a small yad (Yet Another Dialog editor) script which displays a dialog containing several choices for launching a set of related programs. Some are applications installed normally using the Ubuntu Software center and some are java programs called by commands of the form java -jar JARFILENAME.jar. If I launch an application by clicking on a desktop file in /usr/share/applications it launches and puts an icon in the Launcher un (HowTos)