Sometimes, very rarely, I also come across something like this. First, it is necessary to check whether the strings are stuck to the shteg and the agraph. Does the tension of the non-working and working parts of the strings equalize when the tension changes? Do the loops of the string on the wirbel(pin) fit well together?
It happens that when you pull the string and it "sticks" to the pins on the rod, then after a while the tension of the string moves slightly to the non-working part and the formation creeps away a little. To avoid this, you can "massage" the strings around the pins on the rod. (By the way! Are there any cracks around the pins on the rod?)
Also, sometimes for many notes, the string wire goes to two positions in the choir at once, through one pin in a cast-iron frame. And when the formation changes, very rarely, but the string can creep a little from one position to another(This is more likely to be encountered when a new string is being installed.).
Also, in not very tight-fitting loops on the wirbel(pin), tension may be released a little and the system creeps away.
Such problems are most likely to occur with tools that have not been used for a long time and/ or have been standing for a long time without tuning.
I will assume that the wirbels hold the formation well and they do not scroll back after pulling the string. (I hope the tool is working properly in this regard).
If this occurs in a serviceable, good instrument, then I assume that the reason is as follows (1st option): you pull one string, stress is added to the structure and the structure is slightly deformed compensating for the stress. You add more tension with the help of the second string and the structure is slightly deformed even more, respectively, this may lead to some weakening of the first string. Perhaps, with auditory tuning, this is simply compensated automatically, but with the device it can suddenly become noticeable.
The 2nd option may be due to the fact that if you tuned the unison very cleanly, then the three strings may begin to vibrate as a single body. Accordingly, it will be 3 times more massive than the strings individually. And if the body is more massive, then at the same tension it will oscillate with a lower frequency. (this is just my guess and maybe I'm wrong, I don't know).
So I also come across this and just pull up more, so that the height of the unison corresponds to the target setting. Well, an auditory check using intervals is mandatory in such cases.
The author of the application recommends making several tool settings. Especially if a lot of time has passed since the previous tuning. Because the piano is such a system that if you change the tension of one string, then somewhere in another place something will shift somewhere...
upd.. No. 2 wrote incorrectly.. not the summation of masses.. eh.. rather, the synchronous vibration of three strings will move the final node of vibrations a little further, which will lead to a slight decrease in the frequency of vibrations, relative to when one string vibrates, and others are muted.