Yes, there is a problem with transceiver reduced MIF dynamic reconfiguration in Stratix® IV and Arria® II devices when using Quartus® II Software Version 9.1-SP1 and 9.1-SP2.
When using reduced MIF dynamic reconfiguration, and using the 'channel reconfiguration with transmitter PLL select' mode (reconfig_mode_sel = 110), an incorrect tx_dataout and tx_clkout may be produced.
To work around this problem use the 'channel and CMU PLL reconfiguration' (reconfig_mode_sel = 101) mode.
This problem affects simulation and hardware.
This problem will be fixed in a future version of the Quartus II Software.