I have not used the Cygnal chips (too expensive for volume production) but I have learned something about JTAG. If you do not pull up the JTAG inputs with 10k or less, you will get partial program erasures due to noise.
I even (belt and suspenders) put two pins on the board (clk and gnd) and put a nugget on when no programming in progress. I can not say thet the nugget is required, but better safe than sorry.

Erik