Hi,
did you reduced JTAG speed on time?
So from your text, I think your use Windows, correct? Which version? Native or VM?
When did this messages appears? When you open JTAG Chain with Quartus or when you try to program?
From other forum entries "209040 Can't access JTAG chain" this appears when you try to programming, correct?
Which USB Port did you use on your PC? USB1 m USB2 or USB3? You should use USB2 or USB3. Can you try out another USB Port?
Maybe you has some power problem, because modules is supplied over USB. And when you start programming, it needs more power for short time.
Can you get access with JTAG chain debugger?
br
John