There is a known software issue when you enable both "Data Rate Division in TX" and "Channel and TX PLL select/reconfig" modes in the ALTGX_RECONFIG block. The channel reconfiguration will not start in both simulation and device. This issue is associated with Stratix® IV GX/GT and Arria® II GX devices.
The current solution is to enable "illegal mode checking" in ALTGX_RECONFIG instance when both reconfiguration modes are on. This issue will be fixed in future Quartus® II software versions.