Hi,
if anybody else runs into the same problem with an FPGA module:
xc3sprog failed to upload the bitstream to a Spartan 6 LX45, complaining "instruction capture is 0x3f". The JTAG chain itself was recognized, it reported the device correctly.
The cause was insufficient 3.3 V supply voltage on the FPGA board, measured at around 3.08 V. Some modification to the LM1117 adjustment resistors brought it back up to
3.3 V and the board works again.
Don't know if all variants of this regulator have overcurrent protection, maybe it was damaged by earlier abuse.
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