DE1 Basic Computer on Nios II SBT

Hi everyone! I am a beginner with the Cyclone II board. Just got it last week. I tried to implement the DE1 Basic Computer project with the Altera Monitor Program and it works absolutely fine I wanted to implement the same with the Nios II SBT for Eclipse. The project builds and runs but only the Reset button, Red LEDs and the corresponding switches work. The 7 Segment Display and the Green LEDs do not work. On debugging I find that the "8 Second Timer" is never incremented. Is there something wrong with the interrupt and exception handling? Any suggestions?

-------Posted in University Program (that seems to be a better place for this)