It sounds like maybe when you created the schedule, you had selected full page.  In other words, maybe you changed to half page on the settings screen but you never updated the schedule: you can have multiple schedules so the "current" settings don't automatically trickle down to the schedules you have running and you have to update or recreate those.  Are you using the Windows or macOS version?

Regards,
Mike

We've not gotten any similar reports over the years.  Perhaps check the driver settings for each of your scheduled jobs and make sure the media size is correct.  Since some printers will allow you to load a sheet that is a different size than what is defined in the driver, it is possible that there is a mismatch and a "half page" on one media is not a half page on the sheets you are using.  Also check the driver settings for each unclog job and be sure there is no scaling being done inside the driver.

Finally, have you tried just getting rid of the jobs you have and making fresh unclog jobs in case something got corrupted in the setups?

Regards,
Mike