Help - nStatus won't release, EP3C5 custom board

Thanks for your reply, simultaneously I burrowed through other similar threads and found that many had issues with the bottom slug not being connected. I was unsure of this on our board and fortunately had a hole right under the FPGA that was grounded so I put _a lot_ of soldering paste there.

Now the JTAG works but CONFIG_DONE won't come high afterwards, what does that usually indicate? The CONFIG_DONE is, as you can see in the schematics, pulled high by a 10kOhm resistor, but it is also connected to a normal I/O on bank 8 and another 10kOhm pull-up. What are the characteristics of an I/O when the device is not configured?