Want some help NIOSII with Custom logic project..

I'm using DE1 board with quartus 8.1. I want to Implement custom logic with use of PIO ports & Interface it to the PC through NIOSII. I was able to establish a RS232 link easily extending the CII_starter_SD_CARD_AUDIO_DEMO.

But I'm facing problems when adding PIO's for implement my custom logic. for the testings I just added 2xPIO 8bit ports as outputs & one PIO port as an Input. I instantiated them only in

system_0 u0 instance with .inport & .outport notations & used wires to connect them in between.

after generating the SOPC system it synthesize correctly. I can see the system.h file has been updated as I was expected. But when I use IORD function to read the INPUT port it always returns -1(255).

Can't understand whats happening Inside. Pls help me with this.