The mail template implemented with is not working properly with attachment storage file system because the attachment is being named with the full path, in DB storage the attachment is just the name of the file.
So, all the features that are looking for MAttachmentEntry.getName() can be failing because the name is not what's expected. These functionalities can be:
DefaultPrintShippingLabel looking for an attachment name starting with shipping_label
Jasper attachments, subreports, resources
WEMailDialog signature with attached images (this was what caused the research)