I'm not sure why it's not showing up. Do an "ls -l /usr/share/applications" and see if there is a package.desktop file there related to your application. You can "cat /usr/share/applications/yourapp.desktop" and check that the contents are correct. Maybe I am using the wrong category string. You should be eable to find it by Caption in the dash or whatever spotlight type tool you desktop provides.
I'll be posting another version of makedeb (final perhaps) this weekend.
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