In most cases, the flexprint cable is simply broken. Revision B and flexprint are also different in terms of trace impedance, but I didn't yet experience programming failures from it. I remember, that it has been necessary to increase the TCK series termination inside the revision B USB Blaster for reliable operation with some boards.
As a first step, you may want to try a short standard IDC cable (similar to the Terasic one) with the Altera USB Blaster. If it doesn't work, try a TCK series resistor in the USB Blaster of e.g. 33 or 47 ohm.