Hi Amanda,
I feel your pain!
The only time I've seen something similar to this was a problem with the Job ID in the hidden DO NOT DELETE - AutoCrat Job Settings tab on the sheet.
A fix we tried at the time was to delete the data (highlighted below) in the Job ID (Column A) of the Job we were having problems with. Then we reopened Autocrat, selected the job, edited it (passing through all of the set-up options and resaved it). This forced a new Job and Job ID in the hidden sheet. Then we deleted the row for the original Job ID. For our problem it worked, not sure if it will help you, but it's something else to try and may work.
Also, if there are 'extra' jobs in the hidden sheet try deleting them as well.
All the best and I hope you get the reports out.
Ngā mihi maioha
Emma