Harold nailed it, too much nitric.
Especially if you had some black on your copper when it “looked finished” as Pd is slow to cement to completion. Something to consider is that in your effort to cover a small amount of material (in small scale tests) with your solution you may have used the proper proportions of acid to water but used too much volume(hence too much acid). You could have kept the volume the same to cover the material, but used less acid at a higher heat or greater timeframe.
Speaking a little bit as to the cementation of PMs and time frames. I keep all of my chloride, nitric, and sulfuric solution wastes separate after removing values. Then before I process them further for waste disposal, I cement them all to copper for a month or more. It is not a large recovery gained by doing this, but it takes little effort to do so (as long as you have not used excess oxidizing agents) before removing the base metals and then neutralizing the solution for proper disposal. As our old friend Irons likes to say “everything but the squeal”.
More pertinent to the question at hand, when I first started making electrolyte for silver cells is where I really learned this lesson as to silver solubility in nitric at a given temperature. Since I was just learning about silver cells I wanted to be very accurate as to what my electrolyte contained so I used .999 silver to start. My silver was fine grained so should have gone into solution very readily and it is worth noting that I was using ACS grade nitric.
However I found that taking my solutions to a warm temp (think coffee but just a little too hot to drink) and holding that temperature for an hour, left me with undigested silver and a solution that still contained free nitric acid (much to my original dismay). If you try the same thing as I did starting out, and still have silver in the bottom of your beaker, you will be amazed by how much more silver will go into solution at just shy of boiling instead of lower temperatures. It is only after staying at a temperature just below boiling for 20 minutes (based on my experience), that you can be assured of having a nitrate solution completely saturated with silver (if fine silver still remains in the bottom of your beaker) with next to no free nitric acid remaining.
Now be aware that if you are not just trying to be sure of the complete consumption of all nitrates in a dilute solution, but have instead followed what I did above in making a concentrated silver nitrate solution. You must immediately follow your complete digestion of your silver to its saturation point at near boiling, and begin to dilute it with distilled water as it cools, or you will have a beaker filled with a solid mass of silver nitrate crystals.
To be clear, I have not tried to apply this procedure starting with pure Pd and nitric (in this topic it seems that Pd is a possible component), but my gut instinct tells me the results would be very similar. I know I have traveled off of the path of what FrugalEE was asking, but I felt it the best way to answer his questions based on my own experience.
I would love to hear a chemist give a more exacting explanation (a chemist I am not) and we would all learn much more than I can share. I will be honest, when I first came to this forum cementation and the electromotive series of elements rules did not seem to always follow their own laws by my own reckoning. It is only through trial and error that I have been able to make use of the concept. As an example, who here has tried to cement Pd on silver with success, despite what is supposed to happen electromotively?
