Are there any problems with timing analysis for Stratix and Stratix GX designs implemented prior to Quartus II software version 4.1?

Yes; timing analysis should be rerun for Stratix® and Stratix GX designs implemented prior to the Quartus® II software version 4.1. The t_co values reported by the Quartus II software version 4.0 and earlier are inaccurate. The t_co changes for I/O standards with high-current drive-strength settings will be affected less than I/O standards with low current drive-strength settings.

Rerun timing analysis on designs implemented prior to the Quartus II software version 4.1 to identify any I/O timing issues. If I/O timing constraints are not met, refer to the white paper Improving Pin-to-Pin Timing in Stratix & Stratix GX Devices (PDF) for design solutions.

This problem has been fixed beginning with the Quartus II software version 4.1 and it does not affect any other devices.