Why do I see I/O timing violations in HardCopy III devices that were not present in the FPGA version?

In the Quartus® II software version 9.0 SP1 and earlier, delay chain values for HardCopy® III devices are not correctly reflected in the TimeQuest Timing Analyzer. As a result, incorrect timing violations may be reported in I/O timing paths.

To show correct delay chain values in the TimeQuest Timing Analyzer, run the quartus_sta command at a command line with the --force_dat option as follows:
quartus_sta <project name> --force_dat

If you are using the TimeQuest unser interface, run the following command within TimeQuest: 
create_timing_netlist -force_dat

This problem is scheduled to be fixed in a future version of the Quartus II software.