A frustrating little problem. Set up cron so that it runs a script on the required day of every week, rather than on that day every second week. Inside the script put an 'if' statement. Calculate the current day as a number of days since any fixed time in the past, perhaps using date(1) for a bash/ksh/sh script. If the number of days is even, run your fortnightly job. If the number of days is odd, finish without running anything.
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