Cyclone IV JTAG Working, Configuration Not

I eventually ran out of things to try. I went for outside help through an Altera applications engineer, but they also ended up stumped. I scrapped the boards. I've done two more Cyclone IV designs from scratch since then, and both of those worked fine on the first try. The most significant electrical difference on the boards that didn't work was that they used only two power rails (1.2V core and 2.5V VCCA+I/O) instead of three (1.2V core, 2.5V VCCA, and 3.3V I/O). That could be a hint, but I wasn't able to find any reason that a two-rail design would be more problematic than a three-rail design. I figured the problem was just a fluke of some kind (bad PCBs, spoiled parts, or a problem during assembly) and moved on. It stings to be out $400 on non-working prototypes, but it could be worse. At least they weren't Stratix parts.