JTAG trace length affecting programming ability
"@analogsystemsrf When I probed the lines I didn't see much noise or coupling at all. Pretty clean looking to me. In fact, with the probes in place the programming worked better than without."

It sounds like your programming lines might be improperly terminated and that you've got some ringing on them originating from an impedance mismatch somewhere. Probing signals like that can often hide/fix the issue.