The current TDO sampling in usbblaster_transfer() line 262 seems to be very sensitive to signal propagation delays since it read TDO from the device shortly before generating a falling edge on TCK.
Cyclone devices for example update TDO with the falling TCK edge and do not detect when connected to a clone cable (as described on ixo.de). Reading TDO with the rising TCK edge seems to work more reliable.
I'd propose the attached patch to resolve the timing issue.
Move TDO sampling between falling and rising TCK
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The patch has been integrated in branches/usbbl_performance for test purposes.
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Merged to trunk r1273.