JTAG TCK droop using USB Blaster(Ver B) and Cyclone II

The waveform is within LVTTL voltage limits. I remember to have seen a similar waveform, so I think it's normal operation with Rev. B. TCK is nevertheless prone to pick up interferences, e.g. crosstalk from fast edge signals. Different USB Blaster generations behave slightly different in this regard because the utilize different driver circuits. In some cases, small parallel capacitors near the FPGA TCK input (e.g. 10 pF) helped to supress TCK ringing.