Yes, after the release of the Quartus® II software version 9.0 the timing analysis for the M9K block has been updated for the Cyclone® III device family. The update adds the ability to analyze a clock enable path to the M9K block.
To verify if your design is affected by this update follow these steps:
(*) Create the netlist in the TimeQuest Tcl console with the -force_dat option or command line with the --force_dat option. This option is only required with the patched version of the Quartus II software version 9.0 and not version 9.0 SP1.
You can download the script, patch, and related readme files using the links below: