JTAG Programmer using Zedboard - Signal Integrity problems?
Update 20171005: Ok I finally found the problem. Turns out my TMS pin was assigned to XADC-GIO3 (Pin J15) and this pin was the issue. Every other pin H15, R15 (respectively TCK, TDI) has a Vpp of 2.5V while J15 only has ~1point-something volts. I turned this into an input pin by swapping with TDO (K15) and everything turned out fine! No need for twisted pairs or termination or pull-up resistors on any signal - TMS, TCK, TDI or TDO. I was also finally able to program the target board with my Zedboard JTAG programmer.