Please read the documentation....specifically the User's Guide that came with your board!
I just took a quick glance through it, and I don't even think that what you're trying to do is even possible. It looks like your board only boots out of an EPCS16 device.
So... as near as I can tell, your 4MB of CFI flash can be used for software (or other data), but not for an FPGA hardware image. Your hardware should always be stored in the EPCS16 device.
Cheers,
- slacker
EDIT: You _can_ program both the EPCS device and your CFI flash device with the flash programmer. Good news is that your flash programming is working....it's just that your board doesn't support (I don't think) what you're trying to do.