Hi Crossroads. OK. I' posting the entire program below.
You can see the PROGMEM arrays near the top & they are used in the synthesis engine near the bottom. In the wave update stage and in the interrupt. Oh, I have to say I'm using an XAduino board which uses an ATXMEGA128a3 and Arduino 1.0.1 which has been modified for the XMEGA. 
I'vec missed out the MIDI part of the code to shorten the length so it fits. It doesn't have to do with PROGMEM calls anyway..
Hope someone can help.
//Modification of GordonJCP's FMTOY to work on XMEGA128a3.
// Uses on board DAC as opposed to PWM.
//Controlled by Bluetooth through Serial port 0 from an Android tablet.
//Thanks to Erik.T (AVR_Freaks) for the advice on using the DAC.
#include<avr/io.h>
#include<avr/interrupt.h>
#include <avr/pgmspace.h>
#include <stdint.h>
#include <avr/wdt.h>
//#define SERIAL
// table of 256 sine values / one sine period / stored in flash memory
PROGMEM byte sine256[] = {
127,130,133,136,139,143,146,149,152,155,158,161,164,167,170,173,176,178,181,184,187,190,192,195,198,200,203,205,208,210,212,215,217,219,221,223,225,227,229,231,233,234,236,238,239,240,
242,243,244,245,247,248,249,249,250,251,252,252,253,253,253,254,254,254,254,254,254,254,253,253,253,252,252,251,250,249,249,248,247,245,244,243,242,240,239,238,236,234,233,231,229,227,225,223,
221,219,217,215,212,210,208,205,203,200,198,195,192,190,187,184,181,178,176,173,170,167,164,161,158,155,152,149,146,143,139,136,133,130,127,124,121,118,115,111,108,105,102,99,96,93,90,87,84,81,78,
76,73,70,67,64,62,59,56,54,51,49,46,44,42,39,37,35,33,31,29,27,25,23,21,20,18,16,15,14,12,11,10,9,7,6,5,5,4,3,2,2,1,1,1,0,0,0,0,0,0,0,1,1,1,2,2,3,4,5,5,6,7,9,10,11,12,14,15,16,18,20,21,23,25,27,29,31,
33,35,37,39,42,44,46,49,51,54,56,59,62,64,67,70,73,76,78,81,84,87,90,93,96,99,102,105,108,111,115,118,121,124
};
PROGMEM byte sine256_2[] = {
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, };
int main(void)
{
setup2();
initialization();
while(1){
// st=0x90;p1=69;p2=125;
byte note = 60;
byte note2=60;
while(Serial.available()<=12) {
}
// update the voices
phaccu_lfo += tword_lfo;
lfo_icnt = phaccu_lfo >> 8;
lfo = (pgm_read_byte(sine256+lfo_icnt)-127)/128.0f;
eg1 = eg1_rate_level[eg1_phase] + eg1_rate[eg1_phase] * eg1;
if (!eg1_phase && eg1 > 0.98) eg1_phase=1;
eg2 = eg2_rate_level[eg2_phase] + eg2_rate[eg2_phase] * eg2;
if (!eg2_phase && eg2 > 0.98) eg2_phase=1;
gain1 = (current.op1_gain<<1) + (eg1 * ((current.op1_env-64)<<1));// + keyfollow ;
if (gain1 < 0) gain1 = 0;
gain2 = (current.op2_env<<1)*eg2;
dfreq=tfreq;
tword_m1 = pow(2,32)*((dfreq* current.op1_ratio)/2 * (1+(lfo*current.op1_lfo)/256.0))/refclk;
tword_m2 = pow(2,32)*((dfreq* current.op2_ratio)/2 * (1+(lfo*current.op2_lfo)/256.0))/refclk;
phaccu_lfoB += tword_lfoB;
lfo_icntB = phaccu_lfoB >> 8;
lfoB = (pgm_read_byte_near(sine256_2+lfo_icntB)-127)/128.0f;
// lfoB = (pgm_read_byte_near(saw256+lfo_icntB)-127)/128.0f;
eg3 = eg3_rate_level[eg3_phase] + eg3_rate[eg3_phase] * eg3;
if (!eg3_phase && eg3 > 0.98) eg3_phase=1;
eg4 = eg4_rate_level[eg4_phase] + eg4_rate[eg4_phase] * eg4;
if (!eg4_phase && eg4 > 0.98) eg4_phase=1;
gain1B = (current2.op3_gain<<1) + (eg3 * ((current2.op3_env-64)<<1));// + keyfollow ;
if (gain1B < 0) gain1B = 0;
gain2B = (current2.op4_env<<1)*eg4;
//dfreq = portamento*tfreq+(1-portamento)*dfreq;
dfreq2=tfreq2;
tword_m1B = pow(2,32)*((dfreq2* current2.op3_ratio)/2 * (1+(lfoB*current2.op3_lfo)/256.0))/refclk;
tword_m2B = pow(2,32)*((dfreq2* current2.op4_ratio)/2 * (1+(lfoB*current2.op4_lfo)/256.0))/refclk;
//} THIS ONE!!!!
}
}
}
//******************************************************************
// timer2 setup
// set prscaler to 1, PWM mode to phase correct PWM, 16000000/510 = 31372.55 Hz clock
// Serial timer interrupt
//******************************************************************
// Timer2 Interrupt Service at 31372,550 KHz = 32uSec
// this is the timebase REFCLOCK for the DDS generator
// FOUT = (M (REFCLK)) / (2 exp 32)
// runtime : 8 microseconds ( inclusive push and pop)
volatile int out,out2;
ISR ( TCC0_OVF_vect ) {
// internal timer
if(icnt1++ > 31) { // slightly faster than 1ms
do_update=1;
icnt1=0;
}
// operator 1
phaccu1=phaccu1+tword_m1;
icnt=phaccu1 >> 24;
y1 = pgm_read_byte_near(sine256 + ((icnt+fb1) % 256));
fb1 = fb*(y1 + fb1) >> 8;
// operator 2
phaccu2=phaccu2+tword_m2;
icnt=phaccu2 >> 24;
//fb2 = gain1*(y1) >> 8-(gain1>>1);
y2 = pgm_read_byte_near(sine256 + ((icnt+fb2)%256));
fb2 = ((gain1*y1)>>6)-(gain1>>1);
// operator 3
phaccu1B=phaccu1B+tword_m1B;
icntB=phaccu1B >> 24;
y1B = pgm_read_byte_near(sine256_2 + ((icntB+fb1B) % 256));
fb1B = fbB*(y1B + fb1B) >> 8;
// operator 4
phaccu2B=phaccu2B+tword_m2B;
icntB=phaccu2B >> 24;
//fb2 = gain1*(y1) >> 8-(gain1>>1);
fb2B = ((gain1B*y1B)>>6)-(gain1B>>1);
y2B = pgm_read_byte_near(sine256_2 + ((icntB+fb2B)%256));
// set the PWM
out = ((gain2*y2)>>8)-(gain2>>1);
out2 = ((gain2B*y2B)>>8)-(gain2B>>1);
// DC restore and clip output
out += 127;
out >>=1;
if (out<0) out=0;
if (out>0xff) out = 0xff;
out2 += 127;
out2 >>=1;
if (out2<0) out2=0;
if (out2>0xff) out2 = 0xff;
DACB.CH0DATA=(out<<4);
DACB.CH1DATA=(out2<<4);
}