Hello
Just guessing. I don't have the cyclone pro, just multilink. However, the connection dialog of the multilink allows you to select the divider used to derive bus clock vrom the oscillator clock - 2 or 4. Make sure that you select the 4, which corresponds to the divider normal mode. The option affects the value on PTB0 pin during startup. For further explanation see datasheet of the AP32 and chapter Monitor ROM.
Regards
Petr