EPC16 Programs but Fails Verification

I have an EPC16 device on a custom board for configuring a Stratix EP1S60. The board design is an old design and this board was previously working.

The problem I have now is that the EPC16 is recognized by the Quartus Programmer (QII v6.0) and even claims to program successfully (via JTAG), but when I run a verify with the QII Programmer it fails. I have also tried reading back what is stored in the device using the "Examine" feature in the programmer and the .pof file it reads back looks totally different than the .pof file that was supposed to be programmed. (In addition to all this the device doesn't properly configure the FPGA, as you can imagine that is the original problem that led me down this path).

I have tried replacing the EPC16 but that did not fix the problem. I also verified that I am meeting the requirements for the newer Intel based flash (i.e. pins 37 and 41 are NC, etc).

Anybody have any ideas about what can cause this problem?