[ubervexed]

My experience is that certain chars (underscore, and multiple periods) in the book filename triggers the Factory Reset message. Sending a filename that contains these characters to the Touch can be prevented by changing a Calibre setting:

Select Preferences, then Sending bools to devices

Change Save template from {author_sort}/{title} - {authors} to {author_sort[0]}/{id}

This will ensure that both the directory and filename created on the Touch are innocuous.