The MSEL pins in Stratix II devices are internally pulled down via 5k ohm resistance. Pulling an MSEL pin high externally (to VCCPD = 3.3V) via a 10k ohm resistor will present an indeterminate value of ~1.1V to the MSEL pin. This could prevent the device from configuring. Hence you should tie MSEL pins directly to VCCPD (3.3V) or GND. Alternatively you can use a zero ohm resistor to tie them to VCCPD or GND.