We recently started seeing a VERY similar issue with general (not Quickbooks) email templates we use in our Contact Center.  All of the template emails were saved as UNICODE templates and users that were filling in the blanks on the templates found that the entire email sent as JUST the template with no custom information on it.  When our Quickbooks user contacted me about two weeks later with this very issue, but in Quickbooks, it seemed to match up.  Our Network Logical team had recently done an update to the email system (I'm not aware of what the update was), an update that may have also been done by many other companies.  When our Microsoft rep was asked about the unicode email templates, the response was that they "no longer support the use of unicode email templates".  I'm just guessing here, but I suspect that Quickbooks is storing the templates as unicode and outlook no longer likes those unicode templates for some reason.