Cyclone III AS configuration bizarreness

You possibly need an active probe to see the CLK signal undistorbed, The final cause for configuration problems related to JTAG signal quaility is often a non-monotic, ringing CLK edge, which is seen as double clock edge by the JTAG logic. A small capacitive load like the 10 or 12 pF of a standard passive 10:1 oscilloscope probe can be already sufficient to fix the problem.