See below
Based on what info you have given me, I suspect you have an Intel FLASH based device rather than a Sharp/Micron based device (see
http://www.altera.com/literature/pcn/pcn0506.pdf) and there are subtle differences between these variants which you may not be aware of...
If you see
http://www.altera.com/literature/dp/config/epc16.pdf You'll see at the bottom of the table notes (2) & (4) which applies to pin 5 & pins 37 & 41.
For the Intel flash device, pin 5 is a power pin, not byte enable so ensure that you connect this DIRECTLY to VCC & not through a resistor.
Note (4) states that pins 37 & 41 should be N/C for Intel based EPC16 devices.
Finally ensure that Quartus II 5.1 or greater is being used to program the EPC16. (See
http://www.altera.com/literature/wp/wp_epc_flash.pdf). Try regenerating the pof in Quartus II 5.1 or greater if that doesn't help either.
Unrelated to the FLASH vendor types, there are other reasons why you may get an ID error -
Firstly, ensure that the external FLASH pins are not being driven during programming of the EPC16 - see
http://www.altera.com/support/kdb/solutions/rd03202002_6077.html and ensure that You have connected the following pins of the 100-pin PQFP package as follows:
F-A0 -> C-A0
F-A1 -> C-A1
F-A15 -> C-A15
F-A16 -> C-A16
see
http://www.altera.com/support/kdb/solutions/rd03072002_2053.html Hope this helps
