Cyclone II configuration problem

I am debugging a new board which uses an EP2C5Q208C8 and an EPCS4SI8N.

I was able to configure the EP2C5 several times using JTAG, and had many things working. However, the EP2C5 now appears not to accept the configuration - nothing works after configuration, although the programmer seems to recognize the chip, and reports that it successfully performed the operation. If I recall correctly, when the thing worked, data was transferred slowly enough that I could see the progress bar move, but now it just pops up to 100% instantly.

I did try using Active Serial to program the EPCS4, but the EP2C5 doesn't work after that either.

All supply voltages appear correct.

Any ideas? Have I blown the EP2C5? (It was my last one, but I've just ordered more)