Did you shot those wide open? That could have had an effect and stopping it down would certainly be better.
Also, how many times have you done this test and what kind of stand are you using? It looks like you moved the camera ever so slightly between shots here.
Is the spare shutter of the same generation and/or time period? I have no idea if this would be the case, but Copal may have altered the shutter design in terms of leaf and aperture blade placement over the years.
I carry two spare shutters with me for this same reason and have had to swap the shutter in my SK 35mm twice on set. I also swapped out the shutter in my Rodie 55mm and 90mm so I could have the shutters repaired without loosing the lenses.
I have never noticed any ill effects when swapping out shutters, other then the aperture scale is not there to reference. So I typically have to gauge where f/11 is relative to the shutter speed scale on the original and use that as my guide on the new shutter.
I know that the guys at Schneider and Rodenstock will advise against this, claiming that it will effect focus and that each lens is fitted to it shutter. (But keep in mind, it’s there job to be finicky and they’re German.) However, if this were the case, then the front groups of each lens would have to be shimmed so the distance would be precise and I have never found a shim at the front in the dozen lenses I have taken apart. Bob Watkins, at Precision Camera near Chicago (were I get stuff repaired), told me that occasionally you will see a shim in the front. However I feel like this would be for the rare cases where the shutter was just a little thinner then it should be.
I also spoke to the techs at Fotocare about this as well, and they often swap out shutters too. They told me that the critical focus point should not be effected. If the thickness of the new shutter is far off from the last one, you will see a decrease in the depth of field, but I feel like this would be more applicable to long lenses and table top photography.
I once read that Copal said two shutters could be off by as much as 24 microns. Typically ranges like this are three standard deviations from the mean in both directions, so a range of six standard deviations in total, which covers 99.8% of cases, . This means 4 is the standard deviation, and 68% of all variations are 1 standard deviation from the mean, or a range of 2. So more then likely any two shutters will be off by less than 8 microns. This is not that much.
Neither Schneider nor Rodenstock give any torque measurements for screwing in either side of the lens to the shutter. They both just say to screw it in until it is snug. The difference between one person's snugness and another's could be 8 microns. So I have to assume these lenses need to be made with a certain amount of operational variance in the distance between the front and rear.
Point being, unless you are unlucky enough to get one of those shutters that is far off from the mean, I dont think it should matter if you swap out a shutter. Do you have another shutter to test?
