VREFB pin in Cyclone V

Hello,

Since it is mentioned in the Pin Connection Guideline that the pin needs to connect either GND or VCCIO if not used, then I am afraid you can't leave it floating.

Although I can't confirm with you that this is the cause of those faulty JTAG pins, I guess what will happen to the pin if left floating is the output of the buffer logic will be undefined since those pins are voltage-reference pins. It means that the pin should be connected to a valid logic for the hardware to work as expected.