In the Quartus® II software version 9.1 and 9.1SP1, the sdc script is unable to source the "<variation_name>_phy_ddr_timing.tcl" file during compilation if the IP files for ALTMEMPHY or High Performance Controllers for DDR2 and DDR3 SDRAM interfaces in Arria® II GX and Stratix® IV devices are not located in the project top level directory.
The workaround is to place a copy of the <variation_name>_phy_ddr_timing.tcl in the top level project directory.
For the TimeQuest Report DDR command to work, also place a copy of these tcl files in the top level project directory:
3. <variation_name>_ phy_report_timing_core.tcl
If you re-generate the IP, you need to copy over the tcl files again. This issue is expected to be fixed in a later version of Quartus II software.