Cyclone III configuration problem

Some of the observations sound confusing. E.g.: An unconfigured FPGA has weak pull ups on all standard I/Os. You should measure respective VCCIO rather than 1V at these pins (with an usual oscilloscope probe or a digital multimeter). Even 0.8 V for AS pins isn't a normal voltage, cause these pins should be driven either high or low in AS mode, as long as nCE is pulled low as required.

The configuration in EPCS may be invalid, but you should at least observe an initial configuration sequence. Low nStatus indicates POR state, usually. As clarified in the datasheet, one of the startup condition may be missing, correct core voltage or VCCA. You also should check nStatus pullup and possible pin shorts at the board.