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The first time I looked at crontab -l it was blank. I deleted and recreated the schedules in SuperDuper, then got then did crontab -l again and got following (dummy host name substituted)
0 2 * * 0 open file:///Network/Servers/server.example.com/Volumes/Data/Network\%20Homes/download/Library/Application\%20Support/SuperDuper\%21/Scheduled\%20Copies/Smart\%20Update\%20Server\%20HD\%20Backup\%20from\ %20Server\%20HD.sdsp/Copy\%20Job.app
0 3 * * * open file:///Network/Servers/server.example.com/Volumes/Data/Network\%20Homes/download/Library/Application\%20Support/SuperDuper\%21/Scheduled\%20Copies/Smart\%20Update\%20Data\%20Backup\%20from\%20Data. sdsp/Copy\%20Job.app
So, it seems like SD! is creating little custom app bundles that are stored in ~/Library/Application Support/SuperDuper/Scheduled Copies. I checked and those were present (at least after I had recreated the schedules). The question is, why was the crontab blank? If that's getting dumped for some reason, it would explain why the schedules stop.
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