Run into the same/similar issue.
A desktop application launcher wouldn't work. The correct icon didn't show and 
when I clicked on it, I got the same ... trusted warning with only a cancel 
option.
The .desktop file was executable, so that wasn't the issue.
I tracked down the problem to the Desktop being on a partiton marked "noexec."
I solved the problem by copying the launcher to another partition (with no 
noexec flag), and then creating a link to that launcher on the Desktop. The 
application launcher now works and the correct icon shows.

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Can't launch untrusted app-launchers (.desktop) in GNOME
https://bugs.launchpad.net/bugs/572918
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