You are not able to enable "Enable continuous write of all the words needed for reconfiguration" option in the ALTGX_RECONFIG controller due to a software bug in the Quartus® II software v11.0 and v11.0 sp1. The ALTGX_RECONFIG parameter editor allows you to check-off this option but this setting does not take affect internally. If you re-open the ALTGX_RECONFIG parameter editor, you'll find this option un-checked even though you had checked it off previously.
To work around the problem, change the directory to the folder containing the generated ALTGX_RECONFIG parameter editor file and run the following command at the DOS or Linux prompt:
qmegawiz –wiz_override="enable_full_write=true,data_latency=2" <altgx_reconfig file name>
This problem has been fixed starting with the Quartus® II software v11.1