You are not able to enable "Enable continuous write of all the words needed for reconfiguration" option in ALTGX_RECONFIG controller due to a software bug in Quartus® II 11.0 and 11.0 sp1 software. ALTGX_RECONFIG Megawizard™ allows you to check-off this option, but this setting does not take affect internally. If you re-open ALTGX_RECONFIG Megawizard, you'll find this option un-checked, even though you had checked it off previously.
To workaround the problem, change the directory to the folder containing the generated ALTGX_RECONFIG Megawizard 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 issue will be fixed in furture software versions.