Stratix III 3SL150 Holes in Flash

After taking about a month off from working on the flash, I have repeated these steps with success. I initially had problems with the "Can't recognize silicon ID for device 1" errors which took several hours to work through. It ended up that if I set up the board to be programmed through the CPLD USB Blaster, everything worked perfectly. If I used my external USB Blaster device through the JTAG port, no matter what the switch and jumper settings were set to, I got the error after programming the FPGA and before any data was written to the flash. Odd!