In the Quartus® II software version 12.1 and later, there is an issue with the EMIF Toolkit exporting the calibration report in a single file. It only allows exporting of each individual section of the report.
The following workaround can be used to export the full calibration report :
After running the "Generate Margining Report" command, type the following tcl command in the EMIF toolkit console:
write_connection_target_report -id <id_value> -file "<report_name>"
where <id_value> is the Connection ID of the memory interface shown in the Connections Report -> Linked Connections.
An example command is :
write_connection_target_report -id 0 -file "report0.rpt"
This issue has been fixed in the Quartus II software 13.1 release.