Yes; timing analysis should be rerun for Stratix® and Stratix GX designs implemented prior to the Quartus® II software version 4.1. The tco values reported by the Quartus II software version 4.0 and earlier are inaccurate. The tco 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.