I am having issues with JTAG with my Cyclone IV, specifically the JTAG clock. I am trying to change the JTAG clock frequency somewhere, but can't find where this is done in Quartus II.
How can I change the JTAG frequency in Quartus II?
According to this page, unfortunately the answer appears to be no:
Also here the same is mentioned.
Before you do any of the below, try to figure out what your dealing with here. Scope the signal (set to 10x with a tip ground clip - don't use the ground lead.
Quick thoughts on getting it to work (assuming you find some nasty ringing) - I'm guessing you can't shorten the distance of the signal route easily, so try a small capacitor (possibly with a series resistor) to ground on the line (I'd try at the receiving end) to attempt to terminate it roughly (at least enough for it to work)
Let us know how it goes if you do attempt any of this (scope shots are always handy) and good luck.