That works fine here, what version of alacarte are you using?
Do the files in .local/share/applications get edited when you
check/uncheck the box?
** Changed in: alacarte (Ubuntu)
Assignee: (unassigned) => Ubuntu Desktop Bugs
Status: Unconfirmed => Needs Info
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Can't tick off 'Run In Termianl'
https://launchpad.net/bugs/55611