RapidIO IP core variations that target a Stratix IV GX device do not implement the reset sequence recommended in the Stratix IV Device Handbook. However, the reset sequence the IP core implements has been verified in hardware.
This issue has no known design impact.
To avoid this issue, you can modify the clear text source code for the reset controller in your RapidIO IP core variation. The relevant source code is located in the <variation>_riophy_reset.v (or .vhd) and <variation>_riophy_xcvr.v (or .vhd) generated files.
Regenerating your Qsys system overwrites your manual modification of the reset sequence. However, you can maintain copies of the modified files and after you regenerate, replace the new files with the modified files.
This issue will not be fixed in a future version of the RapidIO MegaCore function.