SO Invoice Printing to Paperless Office Errors

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When our accounting department tries to print two batches of SO Invoices they are not processing correctly.  When they do a SO Invoice batch print to pdf it usually emails the customer that are setup to receive the invoices through email, when they try or accidentally print two batches at the same time, one batch does not get emailed or saved as a pdf.  Trying to help them figure out the reason, before we went to the cloud version we didn't have this issue.  I have file lock enabled.