Did this file come in from Family Tree Maker Version 16 or earlier?
The Automatic Reference ID was NOT in Version 2008, 2009, 2010, but was added in Version 2011. It was a feature in Version 16 and earlier. Only Manually entered Reference IDs were carried into Version 2008 and newer, IF they are in Version 16 or earlier.
Did you check the Items to Include options for the report that you are generating?