SPI Problems

Try changing the wait completion loop this way:

do{
    IOWR_ALTERA_AVALON_PIO_DATA(LED_PIO_BASE,countTMT & 0x01);
    usleep(50000);
    countTMT++;
    status = IORD_ALTERA_AVALON_SPI_STATUS(SPI_MASTER_BASE);
}  while( ((status & ALTERA_AVALON_SPI_STATUS_TMT_MSK) == 0)
                || ((status & ALTERA_AVALON_SPI_STATUS_TRDY_MSK) == 0) );

Also check if timing parameters (clock polarity and phase) match master and slave.

Your problem can be possibly due to the fact that slave is missing a clock pulse, then the rx word would be completed only on the first clock pulse of next tx word, thus leading to shifted results.