For Stratix® IV GX and Stratix® IV GT devices, the Quartus® II software verison 9.0 generates this error if there are multiple ALTGX_RECONFIG instantiations which are controlled by the same user logic in a design.
Some designs may not show the above error and pass compilation. However during run time, the dynamic reconfiguration on some transceiver channels may be affected. This issue does not show up in functional simulation. To Fix this issue, Altera recommends you to install Patch 0.19 for the Quartus II software version 9.0. Install the appropriate patch from the link below and compile your design.
Patch 0.19 for Quartus II 9.0 Windows.zip
Patch 0.19 for Quartus II 9.0 Linux.tar
Patch 0.19 for Quartus II 9.0 Linux (readme.txt)
Alternatively, you can work around this issue by using a single ALTGX_RECONFIG block.
This problem is scheduled to be fixed in a future version of the Quartus II software.