Hi Nick,
Have you found a solution yet?
I'm having a similar problem when configuring in AS mode via an EPCS16, where nstatus is pulling low as conf_done rises. This is using a stratix2gx with AES encryption key programmed.
The FPGA does boot however when I leave the ethernet blaster cable connected (I mean physically just the cable, not the programmer!)
Fitting a capacitor of between 66pF and 330pF between conf_done and GND is allowing the FPGA to boot without the cable fitted, just need to know why now!
Let me know if you've found anything different.
Cheers
Andrew