It's impossible to tell what is going on without logging. My suggestion would be to open a case with support and provide them with your current set of logs from the console.
You may also want to setup a quick test against a machine. Create a new Machine Group, add a machine with credentials, schedule a scan (with or without deployment) 5-10 minutes into the future. Does it run?
If I just create a new scan the new task works fine. Same machine group, scan and reboot, no problem.
We may be able to identify something through your current logs, it's possible something didn't transfer over during the upgrade to 9.3.