Transceiver dynamic reconfiguration may fail when the "Enable continuous write of all the words needed for reconfiguration" option is enabled in the altgx_reconfig MegaWizard™ on Stratix® IV GX/GT and Arria® II GX/GZ devices due to a problem with the altgx_reconfig MegaWizard.
Asserting the write_all signal for one reconfig_clk clock cycle may cause the dynamic reconfiguration process to fail with Quartus® II Software Versions 10.0-SP1 and earlier.
To work around this issue, assert the write_all signal for four reconfig_clk cycles, or upgrade to Quartus II Software Version 10.1 or later.